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Table of Contents Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . i address . . . . . . . . . . . . . . . . . . . . . . . . . . . i GETTING STARTED . . . . . . . . . . . . . . . . . . . . . . . 1 BASIC CONSIDERATIONS . . . . . . . . . . . . . . . . . . . . 3 CURSOR MOVEMENT / NAVIGATION . . . . . . . . . . . . . . . . 7 REFERENCE SECTION . . . . . . . . . . . . . . . . . . . . . . 9 CHANGE TYPE . . . . . . . . . . . . . . . . . . . . . . 9 CHANGE NAME . . . . . . . . . . . . . . . . . . . . . . 10 COMPARE . . . . . . . . . . . . . . . . . . . . . . . . 10 COMPLEMENT . . . . . . . . . . . . . . . . . . . . . . . 11 COPY . . . . . . . . . . . . . . . . . . . . . . . . . . 11 CREATE . . . . . . . . . . . . . . . . . . . . . . . . . 12 DELETE SEQUENCE . . . . . . . . . . . . . . . . . . . . 12 DELETE to end of line . . . . . . . . . . . . . . . . . 12 DELETE to end of sequence . . . . . . . . . . . . . . . 12 ERROR MESSAGES . . . . . . . . . . . . . . . . . . . . . 12 FILES . . . . . . . . . . . . . . . . . . . . . . . . . 13 FIND . . . . . . . . . . . . . . . . . . . . . . . . . . 14 GENETIC CODE . . . . . . . . . . . . . . . . . . . . . . 15 GET . . . . . . . . . . . . . . . . . . . . . . . . . . 16 GOTO . . . . . . . . . . . . . . . . . . . . . . . . . . 16 HELP . . . . . . . . . . . . . . . . . . . . . . . . . . 17 HORIZONTAL SCROLL . . . . . . . . . . . . . . . . . . . 17 INPUT . . . . . . . . . . . . . . . . . . . . . . . . . 18 INPUT/OUTPUT commands . . . . . . . . . . . . . . . . . 18 INSERT/TYPEOVER . . . . . . . . . . . . . . . . . . . . 19 JOIN . . . . . . . . . . . . . . . . . . . . . . . . . . 19 LOWER CASE . . . . . . . . . . . . . . . . . . . . . . . 19 MATCH . . . . . . . . . . . . . . . . . . . . . . . . . 19 MOVE . . . . . . . . . . . . . . . . . . . . . . . . . . 20 OUTPUT . . . . . . . . . . . . . . . . . . . . . . . . . 20 PRINT-OUT . . . . . . . . . . . . . . . . . . . . . . . 21 PUT . . . . . . . . . . . . . . . . . . . . . . . . . . 24 PUT ALL . . . . . . . . . . . . . . . . . . . . . . . . 24 QUIT . . . . . . . . . . . . . . . . . . . . . . . . . . 24 RE-DEFINE ORIENTATION . . . . . . . . . . . . . . . . . 25 REMOVE NUMBERS AND SPACES . . . . . . . . . . . . . . . 25 REMOVE SPACES . . . . . . . . . . . . . . . . . . . . . 25 REPLACE . . . . . . . . . . . . . . . . . . . . . . . . 25 REPLICATE . . . . . . . . . . . . . . . . . . . . . . . 26 RESTORE . . . . . . . . . . . . . . . . . . . . . . . . 26 REVERSE . . . . . . . . . . . . . . . . . . . . . . . . 26 SLIDE LEFT . . . . . . . . . . . . . . . . . . . . . . . 26 SLIDE RIGHT . . . . . . . . . . . . . . . . . . . . . . 27 SAVE . . . . . . . . . . . . . . . . . . . . . . . . . . 27 SCROLL . . . . . . . . . . . . . . . . . . . . . . . . . 27 SPACE IN 3 . . . . . . . . . . . . . . . . . . . . . . . 28 SPACE IN n . . . . . . . . . . . . . . . . . . . . . . . 28 TAB . . . . . . . . . . . . . . . . . . . . . . . . . . 28 TYPEOVER . . . . . . . . . . . . . . . . . . . . . . . . 28 TRANSLATE . . . . . . . . . . . . . . . . . . . . . . . 29 UNDO . . . . . . . . . . . . . . . . . . . . . . . . . . 29 UPPER CASE . . . . . . . . . . . . . . . . . . . . . . . 30 VERTICAL SCROLL . . . . . . . . . . . . . . . . . . . . 30 WALLS . . . . . . . . . . . . . . . . . . . . . . . . . 30 WIPE . . . . . . . . . . . . . . . . . . . . . . . . . . 30 ESEE The EyeBall Sequence Editor Version 1.04 Copyright (c) Eric Cabot 1987,1988,1989,1990 All Rights Reserved. The author, Eric Cabot, makes no warranty, express or implied to you or any other person or entity. The author will not be liable for incidental, consequential or other similar damages arising through the use of this manual or the software described herein. Preface My original intent in creating a multiple sequence editor was to provide scientists with a basic word-processor for rather routine and naturally obvious editing and presentation tasks because none was available. As you use ESEE please forgive me for providing any but the bare basic tools necessary for actual sequence analysis. There are so many ways to analyze data that I have had to, perforce, leave all decisions about what to actually do with the data in the hands of individual users. This, of course, has permitted me to primarily concentrate on editing problems, per se, and in addition has certainly hastened the release of ESEE to a needy world. Hopefully, these trade-offs will seem worth it. I would like to thank all of the early ESEE users for their patience, criticisms and suggestions. Without the contributions of those many individuals, the program's quality most assuredly would have suffered. Special thanks are due to: A.T. Beckenbach, D. L. Baillie, M.J. Smith, W. Kelley Thomas and J. Boom. Delaney Software Ltd. is also to be thanked, not only for providing the sequence database routines used by the program SEQNCE, but also for permitting any modifications that were deemed necessary. If you are reading this and are not a registered user of ESEE then you are fortunate to have gotten something for nothing; you're welcome. Please address all correspondance to Eric. Cabot Department of Biology University of Rochester Rochester, NY, 14627 I would be pleased to hear from any users, registered or not, who may have uncovered a bug in the program. So why bother registering? The most significant reason is that update and other useful information is sent directly to any registered users. Since little bugs do pop-up now and then, ESEE is gets revised on a frequent basis. For the time being, updates are being provided, free of charge, to registered users, by request. i ESEE Owner's Manual GETTING STARTED 1 GETTING STARTED The EyeBall Sequence Editor (ESEE) is a multi-sequence editing program specifically developed for the entry, manipulation and presentation of nucleic acid and amino acid sequences. The program always treats sequences as independent entities and refers to each only by number and cursor position. When you first enter the editor there is one empty sequence of type N. In order to use additional sequences they must be created or input. There are three ways to input data: INPUT, RESTORE or GET. If you input when there is only one sequence, and that is empty, then that sequence is replaced by the new material. There are six ways to create new sequences: CREATE, REPLICATE, COMPLEMENT, COMPARE, and MATCH. ESEE is entirely memory resident and therefore need not be in the current directory at start-up time. (The current directory can be changed from within the filer window.) The very first screen that you will see has a key piece of information: the maximum number of sequences that you will be allowed to use based upon the amount of memory that is available after loading the program, which requires 140 kilobytes of memory to run with a single sequence. Each additional sequence requires approximately 18.5 kilobytes. Users with only 256K are limited to 7 sequences. While you are in the editor you can get online information by depressing F3. If, at any time, the file ESEEHELP.FIL is not located in the current directory then you will be prompted for a path name for the directory in which the help file is located. Once you have specified the correct path the program will not re-prompt you for a path to the help file unless you inadvertently "loose track" of the help file by changing the current directory. You can change the current directory at will through the FILER window. You can also get help from within the PRINT-OUT window. The sequence on which the cursor resides at any time is considered the current sequence. Most of the editing commands, including most of the cursor movement commands, work only with the current sequence. You can navigate to other sequences with the up- and down-arrow keys. These keys also cause the screen to scroll at the borders of the editing area. The current sequence does change when you scroll. Certain commands (DELETE, INPUT, GET, REPLICATE, WIPE, and COMPLEMENT) may change the current sequence. The pages displayed in the editor refer to screen pages not to pages of print-out which are handled separately. The last page is dynamically calculated as the number of sequences in use changes. This page always includes the position 18,000. 1 ESEE Owner's Manual GETTING STARTED 2 As the number of sequences in use increases, the number of lines of sequence that can be displayed on a screen page decreases. With 10 or more sequences, only one line (60 positions) of each is displayed. Quit the program by typing <ESC>, <RET> (i.e. the "ENTER" key), or F10. You can exit most of the windows with <ESC> or F10. In the case of the Genetic Code Window you must exit by typing <RET>. The <RET> key is used to abort most of the editing commands but there are a few exceptions, notably GET, PUT, and FIND. Read the prompts carefully until you become familiar with the various commands and features of ESEE. A final note, if anything "weird" happens to the display while you are editing try using UNDO to correct any problem then try updating the screen display by changing pages or going into one of the four available windows. If you do discover a bug the author would like to hear about it AS SOON AS POSSIBLE since every effort is made to maintain a stable piece of software. It does not matter if you are a registered user or not, REPORT ALL BUGS, please. 2 ESEE Owner's Manual GETTING STARTED 3 BASIC CONSIDERATIONS Sequences: The editor treats each sequence as a long numbered list of characters. The number assigned to a sequence reflects its position as displayed by the editor, with the highest numbered sequence on the bottom and the lowest (i.e #1) on top. Every single character shown on the screen, including spaces, walls, punctuation and other chemically nonsensical characters, is considered a member of the sequence and is duly assigned a sequence position. Current Sequence: The sequence on which the cursor resides at any given time. Sequence Position: Any possible numbered location for a character in a sequence. The positions are numbered starting at position 1 at the top left of page one and proceeding to rightward and downward. Please note that insertions/deletions invariably cause changes in the numerical positions of all sequence elements downstream of the point of the insertion/deletion. It is possible to assign a meaningful number to the start of a sequence, to be used by the print-out process. Current Position: The cursor position relative to the start of the current sequence. It is quite possible for the current position to be beyond the end of the current sequence. End of Sequence: One position beyond the last actual character in a sequence. The editor displays the end of sequence as a "happy face". Many operations, including all of those that change sequences, will be inhibited if the current position is beyond the end of sequence. It is possible to insert, delete or backspace while the cursor is at the end of sequence itself. Up Stream: Towards the left and/or up. By default the upstream end is 5-prime for nucleic acids and amino for proteins. Down Stream: Towards the right and/or down. By default the downstream end is 3-prime for nucleic acids and carboxyl for proteins. 3 ESEE Owner's Manual GETTING STARTED 4 Orientation: Forward orientation (the default) means that the a sequence is displayed in a 5-prime to 3-prime orientation (amino to carboxyl for polypeptides). The editor indicates forward orientation with the symbol " " displayed to the immediate left of sequence. The symbol for reverse is " ". You can either REVERSE a sequence or REDECLARE its orientation, but ESEE almost always works from left to right with no regard for the chemical orientation. So remember: downstream is to the right and not to the 3' end. Processive Commands: Several of the ESEE commands work in a manner that is termed "processive", meaning that the action of the parti- cular command begins at the current cursor position. Pro- cessive commands always work in a downstream direction, no matter what the orientation of the current sequence. The following is a list of all the processive commands: FIND REPLACE SPACE in n Space in triplets REMOVE SPACES REMOVE SPACES and Numbers TRANSLATE DELETE to End Of Sequence TAB DELETE to End of Line Shift-TAB JOIN Most of the processive commands terminate at the end of sequence but in the case of TRANSLATE, the spacing commands, and the REMOVE SPACES command, the point of termination may be influenced by walls. (Note: The action REMOVE SPACES AND NUMBERS is unaffected by walls.) Walls: Walls cause the premature termination of translation or of the spacing commands. In order to stop translation the wall must be on the product sequence (i.e. the polypeptide), not the template. Downstream from the first wall encountered during translation, the sequence remains unmoved and unchanged. If a wall is encountered at some position in the template, a blank is inserted at that position in the product. The REMOVE SPACES command also terminates if walls are found. Downstream of the wall the sequence remains fixed and any blanks that were removed by the command are re-inserted immediately upstream of the wall. 4 ESEE Owner's Manual GETTING STARTED 5 Sequence Types: There are four valid types of sequence: N, P, T, A which respectively stand for nucleic acid, polypeptide, triple-letter coded polypeptide, and anything else. The most important differences between the way that the different type sequences are treated are summarized below. Print-out numbering: At the time of print-out every single character of a sequence is numbered except for sequences of type T, in which case the number of characters on a print- out line is counted and divided by three. This procedure does not guarantee to produce the correct numbering. For this reason the numbering on T-type sequences is suppressed, by default and it is strongly recommended that you not number type-T sequences. Translation: The template for a sequence must be type N. The translation product must go on a sequence of either type P or type T. COMPARE and MATCH: You can only COMPARE/MATCH sequences of the same type. You cannot use COMPARE/MATCH with type-A sequences. Spacing: Triplet spacing works differently for type-P sequences in order for them to be properly aligned with nucleic acid sequences that are triplet spaced. Upper and Lower Case: For the most part, upper and lowercase are freely interchangeable in sequences. Names: A sequence name can be up to 64 characters, only the first ten characters of which are displayed by the editor. At print-out time you can control the width of the name field. It is highly recommended that you use names to identify your sequences as soon as they are brought into use but naming is strictly optional. It should be noted that, even if you don't use any names at all, space will be reserved for the name field on every line of the printout unless the width of the name field is zero. This feature is explained in more detail in the section describing printing in this manual. 5 ESEE Owner's Manual GETTING STARTED 6 CURSOR MOVEMENT / NAVIGATION HOME moves the cursor to the first position on the current line of the current sequence END moves the cursor to the last position on the current line of the current sequence Page Down goes down a page, unless you are already on the last possible page...the position of the cursor on the screen does not change but the current position increases by the number of positions that can be displayed on a page Page Up works just like Page Down except in reverse Right Arr shifts the current position downstream by 1 Left Arr shifts the current position upstream by 1 Up Arr moves the cursor up one sequence, if the top of the screen is reached the screen scrolls down by one group of sequences if possible Down Arr moves the cursor down one sequence, if the bottom of the screen is reached the screen scrolls up by one group of sequences if possible cnt-HOME takes the cursor to the top-left corner of the screen on the current sequence cnt-END takes the cursor to the bottom-right corner of the screen on the current sequence cnt-PgDn takes the cursor to the last possible page...the screen position of the cursor does not change although the current position does cnt-PgUp works like cnt-PgDn but the cursor moves to page 1...if the cursor is already on page 1 then the cursor moves to position 1 of the current sequence cnt-right shifts the current position downstream 10 positions cnt-left shifts the current position upstream 10 positions 6 ESEE Owner's Manual CURSOR MOVEMENT / NAVIGATION 7 alt = shifts the current position to a specified position cnt-<RET> shifts the current position to a the end of the current sequence ] SLIDEs the current sequence downstream by one position without changing the cursor's position on the screen, sliding has the effect of horizontally scrolling the current sequence relative to any other sequences [ SLIDEs the current sequence upstream 7 ESEE Owner's Manual REFERENCE SECTION 8 REFERENCE SECTION CHANGE TYPE alt-F4 or alt-T This command allows you to re-designate the type of the current sequence. Any sequence may be designated as any of the four valid types. When CHANGE TYPE is evoked, the cursor is positioned in the type field on the current line. You are prompted to enter either a letter corresponding to a valid type, or to cycle through the list of types using the cursor-pad arrow keys. The down and left keys take you one way through the list and the up and right keys take you the other way. Selection is made by typing <RET>. If you accidentally call up CHANGE TYPE then typing <RET> will return you to edit mode with no change. The valid types are: N: nucleic acid P: protein in single letter abbreviation T: protein in triple letter abbreviation A: anything else The type of a sequence may affect certain commands as detailed below (also see the discussion of sequence types in the Basic Considerations section above). TRANSLATE will only work if the current sequence is of type T or P and there has to be a sequence of type N somewhere above (i.e. a lower sequence number) the T or P sequence to act as a translational template. COMPARE and MATCH can only be used of two sequences of the same type, and the type cannot be type A. At print-out time, the type of a sequence can influence the default setting of the option "suppress numbering". 8 ESEE Owner's Manual REFERENCE SECTION 9 CHANGE NAME cnt-f4 or alt-n This command allows you to assign, change or display the fullname of a sequence. The maximum name length is 64 characters, only ten of which are displayed in edit mode. You are encouraged to name your sequences as soon as they are created or input to avoid any possible confusion between sequences. If you inadvertently summon up CHANGE NAME simply typing <RET> will return you to edit mode leaving the previous name intact. The print-out window allows you the option of setting the width of the name field at print-out time. When entering names do not type beyond the end of the name field window because the name that you have just typed will become invisible until you finish entering the new name by typing <RET>. You can cause a name to be blank by typing <SPACE> one or more times followed by <RET>. If you change your mind while entering a new name then type <ESC> <RET>. This will restore the original name. COMPARE shf-F6 This command creates a new sequence that is the result of the comparison of between the current sequence and the first sequence of the same type that can be found above. If, for example, the current sequence is sequence #6 and it is type N, sequence #5 is type P, and sequences #1, #2 and #3 are type N, COMPARE will compare sequence #3 to the current sequence. The result of COMPARE is displayed as a newly created sequence of type A and it is put immediately below the current sequence. The COMPARE result is a dot when the two compared sequences are the same at a position and when they differ, the character at that position in the current sequence is produced. If you don't like dots then you should navigate to the beginning of the resulting sequence and use REPLACE to change the dots to some other character. COMPARE is most useful for showing differences between very closely related sequences. If the sequences are very different you might consider using MATCH instead. COMPARE and MATCH are not case sensitive, meaning that upper- and lowercase versions of the same letter (eg. G and g) will be reported as the same letter. This can give some spurious results when comparing triple-letter coded proteins -- be warned. 9 ESEE Owner's Manual REFERENCE SECTION 10 COMPLEMENT F5 If there is enough room and memory a new sequence is created that is the complement of the current sequence. The new sequence becomes the current sequence and is displayed in the forward orientation. Only sequences of type N may be complemented. Only the following characters produce complements: G, A, C, T, N, R, Y. All other characters are simply copied to the new sequence as is. Case is not significant in complementation but the it is preserved in the characters of the complement sequence. COPY F7 This command is designed to let you mark off a contiguous section of sequence, a copy of which can be inserted at any location in any sequence, provided that there is room to hold the insertion. Once you finish marking, the copy is stored in memory and you are free to change the area that was marked. Note: highlighting is turned off when you finish the marking. After marking you are free to use any other ESEE commands before you retrieve the copy. The copy process can be interrupted at any time simply by typing <ESC>. To mark text use any of the following keys and finish marking by typing either <RET> or F7. Next navigate to the insertion point and type either <RET> or F7. Right Arrow .... marks and highlights a single downstream character Down Arrow .... marks the next 60 positions (i.e. down one line) END .... marks all positions between the current position and the end of the line PageDown .... marks all positions between the current position and the bottom of the page. Left Arrow .... unmarks the rightmost marked character and backs the cursor up by one position. You cannot mark a new block without either completing the copy process or aborting it with the <ESC> key. 10 ESEE Owner's Manual REFERENCE SECTION 11 CREATE alt-C or alt-F8 This command creates a new sequence of type N at the cursor location and designates it as the current sequence, providing (A) that there is enough memory and (B) there fewer than the maximum number of sequences (=21) currently in use. If the cursor was on the highest numbered sequence than you are prompted to choose between inserting the new sequence above the bottom sequence or appending below. In all other cases the current sequence and all those below it are "pushed" down by one to make a hole in which to insert the new sequence. DELETE SEQUENCE alt-D or shf-f2 This command deletes the current sequence. You are always prompted to confirm if you really wish to perform such a destructive task since your data is sacrosanct. If you delete every single sequence a new empty sequence of type N is created as sequence #1. DELETE to end of line cnt-Y (Processive COMMAND) The current sequence is deleted from the position of the cursor to the end of the current line. DELETE to end of sequencecnt-Z (Processive COMMAND) This command is similar to DELETE sequence except in two regards: (A) you are not prompted for confirmation, and (B) the deletion begins at the current cursor position and moves downstream until the end of the sequence is encountered. The cursor position becomes the new end of sequence. ERROR MESSAGES Errors are usually reported on the bottom line of the display. These messages are displayed for 2 seconds. If you depress any key when an error message is displayed, it will disappear immediately. If the key pressed generates the same error then you get the error message again. Messages that say "INHIBITED" are only displayed for 1.5 seconds. In some cases the error messages are displayed at the top of the screen. This is usually when there is a very long or important message. 11 ESEE Owner's Manual REFERENCE SECTION 12 FILES alt-F or shf-F3 The filer window allows you to perform file management tasks without leaving the program. It always displays the current drive and directory on the bottom line of the window. This information is updated if the current directory is changed with the Change Directory sub-command. Exit the filer window by typing Q or <ESC>. The filer sub-commands are listed below. DIRECTORY d ERASE e CHANGE DIRECTORY c RENAME r LOOK l These sub-commands all work pretty much like their DOS equivalents. If you change the current directory you may have to specify a new path to the helpfile ESEEHELP.FIL. The directory sub-command shows filenames highlighted and sub-directory names dimlighted. The LOOK command will display a disk file using a window that is 60 columns wide and 11 rows high. It is not possible to look beyond column 60 of any file. This command can be useful to check that and output or save operation was successful. You can also look at the ".sin" file of a sequence database to see the names, types and lengths of the database entries. 12 ESEE Owner's Manual REFERENCE SECTION 13 FIND f8 (Processive COMMAND) This command will move the cursor to the start of the first occurrence of string of up to 25 characters in length. If the string cannot be found in the current sequence then the cursor does not move, and a message to that effect is briefly displayed at the bottom of the screen. The first time you use FIND there is no previous search string so you are prompted to supply one. At this point you can type <RET> to abort the FIND or you can enter a new string. During entry you are permitted to use the backspace key to delete mistakes. You can start over by typing <ESC>. Subsequent FINDs will attempt allow you to reuse the previous search string, should one exist, if you so desire. If one does exist, then there are three choices: <RET> to reuse the previous string, <ESC> to abort, or anything else to enter a new search string. In the latter case you will be presented with the same prompt as when there is no search string, as described above. You can put walls into search strings by holding down the alt key while typing the number 222 with the keyboard's number pad. A second way to find walls is to actually use the ctrl-backspace keystroke for walls as you enter the search string. If the second approach is used then walls will be represented by a character as you are typing. Subsequent finds will correctly show a wall character in the search string. 13 ESEE Owner's Manual REFERENCE SECTION 14 GENETIC CODE alt-G or alt-f3 The GENETIC CODE window displays and allows changes to the genetic code that is used for translation. There are really only two non-exclusive options in this window, entry of new codon usages either from the key-board and/or from one or more disk files. To change the genetic code from the keyboard simply type in a valid nucleic acid codon in either upper or lower case. Non valid codons will be ignored at this point. Next you will be prompted for a three letter then a single letter code for that codon. If you enter a different number of characters for the prompts you will be re-prompted. For the single and triple letter codes they are taken literally in terms of case and also what letters you choose to use, no matter how "non-standard". The codon files are very simple ASCII files. Each line in a codon file should be of the format: CCCxTTTxS where CCC stands for a valid codon, TTT is for the triple letter code, S is for the single letter code and the x stands for any character at all, but usually a blank or an equals sign is used. If the CCC field specifies a codon that is not valid then the line is ignored, just as it is when entering codes from the keyboard. The files NEWCODE.1 and NEWCODE.2 that are distributed with ESEE are sample codon files that demonstrate the valid use of rather unusual triple and single letter codes. Exit the GENETIC CODE window by typing <RET> when being prompted for a codon to change. 14 ESEE Owner's Manual REFERENCE SECTION 15 GET cnt-F9 This command retrieves a sequence from a database that is designed to work with the SEQNCE program of Delaney Software, Ltd. The PUT and PUT-ALL commands also generate SEQNCE-databases. This feature allows you access to all of the major nucleic acid and protein databases that Delaney Software distributes. In the case of the nucleic acid databases (such as EMBL and GENBANK) the databases are compacted reducing their sizes by a factor of four compared to the original ASCII format. The first time that you use GET you are prompted to specify a database. If the one specified does not exist then the GET command aborts. Subsequent GETs give you the option of using the same database or specifying a new one. Next you are prompted to specify the name of the sequence that you want to GET. The name can be up to 64 characters. A blank name will cause the GET command to abort. Unfortunately, there is no way to list the directory of a SEQNCE-database from within ESEE. You can, however, see what names are in a database at the DOS level by TYPE-ing the ".sin" file of the database. It is not recommended that you use an text-editor on the ".sin" files -- if you inadvertently change the ".sin" file then the database may be adversely affected. See PUT and PUT-ALL for more information on SEQNCE databases. GOTO alt = This command is a special navigation command that causes the cursor to move to a new current position that you select. You are prompted to give the number of the new position. If you try to go to a position beyond the last possible page, then the GOTO will be ignored. The current sequence is not changed by GOTO. 15 ESEE Owner's Manual REFERENCE SECTION 16 HELP F3 Help is available from either the main Edit window or from the Print-out window. (Later releases will probably also have help available from the other windows.) There are currently three pages of edit help and two pages of print-out help. You might like to print out the first part of the help file since it has a useful keyboard template. If you have somehow lost your help file then you can either write one or contact your distributor for a replacement. Make sure that the version number of your copy of the program (shown on the logo panel at start-up time) and the version number on the first page of the edit-help screen are the same. If the file ESEEHELP.fil cannot be located in the current directory then you will be prompted to designate a path to the help file. It is recommended, but not mandatory, that you use as complete and explicit a path designation as possible so as to avoid confusion if you change the current drive and or directory. For example, suppose the current directory is C:\SQLIB and ESEEHELP.fil is in C:\ when you run ESEE. The very first time you summon help you will be prompted for the path. Suppose you answer ".." or "\" and then change the directory to D:\adir. In this case, you will again be re-prompted for the help path if you summon help. The proper response should have been "C:\". Within the help window you can type F3, alt-H or Pagedown to see the next screen. Any other keys will return you to the editor at the current sequence position. If you give a copy of ESEE to someone else the author would be grateful if you would make a point of distributing the help file as well. The help file should not be renamed (although ESEE.EXE certainly could). HORIZONTAL SCROLL LEFT [ Please see SLIDE LEFT. HORIZONTAL SCROLL RIGHT ] Please see SLIDE RIGHT. 16 ESEE Owner's Manual REFERENCE SECTION 17 INPUT alt-I or alt-F9 Read an ASCII file in as a new sequence, if there is enough memory and sequence space. If the current sequence is the highest numbered sequence then you are prompted to append or insert. Otherwise the new sequence becomes the current sequence (without moving the cursor) and all sequences below that point get pushed down. If there is only one sequence and that is empty then the new sequence will replace the original sequence. INPUT/OUTPUT commands INPUT COMMANDS: alt-I, alt-F9 INPUT: Read a sequence from an ASCII file. alt-R, sh-F9 RESTORE: Read in one or more sequences from a file that was saved with the SAVE command. cnt-F9 GET: Get a sequence from a database designed to be used by the program SEQNCE. OUTPUT COMMANDS: alt-O, alt-F10 OUTPUT: Write a sequence to an ASCII file. alt-S, sh-F10 SAVE: Save all sequences, with their names, numbering, and type specifications, to a special "save" file. shf-F1 PUT: Send a sequence to a database formatted for use by the SEQNCE program. cnt-F2 PUT ALL: Send all sequences to a SEQNCE database. 17 ESEE Owner's Manual REFERENCE SECTION 18 INSERT/TYPEOVER This is a toggle. It is recommended that you use insert mode most of the time as there is no undo command available and typeovers can be both destructive and confusing. It is particularly important that you check to see that you are not in TYPEOVER mode when you put in walls. TAB and Shf-TAB are destructive in TYPEOVER mode, meaning that blanks will overwrite the current sequence beginning at the current position. This feature can be useful for quick deletions. JOIN shf-F7 (Processive COMMAND) Joins the current sequence to any sequence that you choose, starting at and including the current position. You can JOIN a sequence to itself, doubling its length and creating a direct repeat. To join an entire sequence, move the cursor to position 1 before using JOIN. LOWER CASE cnt-F6 (Processive COMMAND) Converts any letters to lowercase, beginning at the current position on the current sequence and terminating at the end of sequence. Please consult the entry for UPPER CASE for more information. MATCH F6 Works just like COMPARE except that (A) the resulting sequence is put immediately above the current sequence, (B) if there already is a sequence of type A above the current sequence, it will be replaced by the result of the MATCH, and (C) the results are displayed as vertical bars in positions that are the same (irrespective of case), and as a blank where they differ. As with COMPARE, you cannot use MATCH when the cursor is beyond the end of the current sequence or if there is insufficient room to create another sequence. Please consult the entry for COMPARE for more information. 18 ESEE Owner's Manual REFERENCE SECTION 19 MOVE alt-M or shf-F8 The current sequence is moved, becoming the sequence specified, by number, in response to a prompt. The current sequence is essentially plucked out of its current position, relative to any other sequences, and re-inserted at the new location. One of two things will happen to the sequences below the insertion point, depending on the number of the target sequence relative to the current sequence. If the target number is greater than that of the current sequence, then all the sequences displayed below the current sequence, up to and including the one bearing the target number, will have their numbers decreased by one. If the target number is less than that of the current sequence, all of the sequences below the current sequences have their numbers increased by one. OUTPUT alt-O or alt-F10 Send a copy of the current sequence to an ASCII file (or device). At the end of each line of output, the ASCII code CR/LF is sent to the file. The width of each line is determined by the setting of Line Length in the Print-Out Window. The default width value is 60. If the specified output file already exists you are prompted to select one of three choices: overwrite the existing file, append the current sequence to the existing file, or abort the command. Appended sequences always begin on a new line in the file. If a DOS input/output error occurs during the output process, nothing will be output if the destination is a file, if it is a device, some of the output may get through. 19 ESEE Owner's Manual REFERENCE SECTION 20 PRINT-OUT alt-P or alt-F7 The PRINT-OUT window is used to create formatted print-outs. Each of the sub-commands of PRINT-OUT is detailed below DESTINATION: Specify a file or a device. Don't use colons in device names, i.e. use names like PRN, LPT2 and CON not names like PRN:, etc. Unlike OUTPUT and SAVE, PRINT-OUT will overwrite an existing file with no query. Set the destination to CON to preview the print-out. If you type <CNT-BREAK> when printing to CON you will cause termination of execution of the editor, taking any unsaved sequences with it so BEWARE! TITLE: Enter a string of up to 80 characters to be printed on the top of each page. Note: The title takes up 4 lines of the print out even if it is blank (the default). Line length: Specify the number of sequence characters to include on a line. This setting also affects the format of files written with the OUTPUT command. When calculating the length of line to use keep in mind that some of the other print-out settings will also affect the horizontal format. You have to allow spaces for the left margin, for the name-field + 1 space and also for the numbers + 1 space (if not suppressed). Page length: Specify the maximum number of lines to print on a page. Remember to allow 4 lines for the title and whatever is required by the top margin. Groups of sequences are not split over pages. After each page a form feed is sent. The number of lines that will fit on a page can be influenced by the vertical spacing used by your printer. Print Blank Lines: By default any lines that contain only blanks are not printed. If this option is set to 'Y' then blank lines will appear in the output. Sequence numbers never appear on blank lines. Read Printer File: It is possible to read a file containing settings for the print-out window. See Save Printer File below for more information on saving printer files. 20 ESEE Owner's Manual REFERENCE SECTION 21 Save Printer File: This command creates a special file containing all of the settings of the print out window, including the settings of the printer-command sub-window. The only exception is the list of sequences with numbering suppressed since this is really an attribute of the actual sequences in use at any given time, rather than a printer setting, per se. Suppress Form Feeds: This is useful for getting two or more outputs on a single page. Suppress Numbering: Enter the number of a sequence that shouldn't be numbered. By default numbering is suppressed on T and A type sequences. Unsuppress by "suppressing" a given sequence a second time. You may add as many valid sequence numbers to this list as you desire. Vertical spacing between groups of lines: Enter a value from 0 through 25. Printer Command: Selected presets are highlighted. Selecting a printer preset a second time unselects the option. In addition you may enter an ASCII string of up to 255 characters containing control codes for your own printer. These codes are sent before your sequences. Enter nonprintable characters as decimals in square brackets. This string can be added to as you go along. <RET> alone will clear any existing string. Name Width: Sets the width of the name field for purposes of print-out. Valid values are in the range of 0 to 64. A blank space is always left between the name field and the beginning of the sequences unless the field width is 0. Go: Starts printout. Printing is complete when the word "GO" disappears. You can interrupt the print-out by typing any key when the GO window is displayed. 21 ESEE Owner's Manual REFERENCE SECTION 22 Additional Print-OUT information: By default only sequences of type N and P are numbered on print-out. If the sequence is type T and numbering is unsuppressed then the numbering is the same as for type N except that the count is divided by 3 with the remainder ignored. Sequences of type P will be numbered correctly. Beware of destroying any previous data by printing-out on top of an existing file. No attempt is made to stop you from doing this so be careful. If you print-out to a file without a sufficiently large setting of page length then you risk having form-feed characters put into your file. This may be unacceptable when you try to read the printed file into some word processors. Remember, WALLs are not printed. You have to replace them with specific characters if they are required as place-holdlers. If you need to have special formatting features such as underlining, bold,font changes, etc. then use print-out to a file and read the file into your favorite word processor as if it were any normal ASCII file (which it will be except for embedded form-feeds and any printer commands that you have defined or selected). Don't forget to set-up the format of your word processor program so that it will accommodate the length and width of your print-out, and then read-in the file printed-out from ESEE. For example failure to extend the left margin to suit a wide print-out could potentially scramble your text with wrap-arounds. 22 ESEE Owner's Manual REFERENCE SECTION 23 PUT cnt-F10 The PUT command sends the current sequence to a database that can be used by the GET command as well as by the program SEQNCE (produced and distributed by Delaney Software, LTD.) This section of ESEE was provided by Delaney Software. The first time that you use PUT you are prompted to specify a database. If the database doesn't exist it is created (even if the PUT later aborts for some other reason). Subsequent PUTs will allow you to use the previous database or specify a new one. The databases consist of two files: one with a suffix of ".sin" and one with the same prefix but with a ".sqn" suffix. During PUT, sequences of type A and T are converted to type o. If you later use GET the sequence will become type A. Therefore you should change the type of a T sequence back to type T from type A after a subsequent GET. (NOTE: the SEQNCE program does not normally store protein sequences in triple-letter codes). If the sequence is nucleic acid and is all in uppercase then PUT will compact it resulting in a four-fold reduction in disk-space. If the current sequence does not have a name then you are prompted for one. If you type <RET> in response to this prompt then the PUT aborts. If the sequence is in the file already then there are two choices, delete the one already there or abort the PUT. (Please see GET for more information.) PUT ALL shf-F1 This command works just like PUT except that every single sequence is sent to the specified database. The prompts are all the same. QUIT alt-Q or F10 or <ESC> You are prompted for confirmation before exiting the editor. You must answer with a "Y" or "y" in order terminate the editing session. Be aware that all sequences in memory will be unaccessible once you leave the program. It is, therefore, highly recommended that you back-up your work with SAVE, OUTPUT or PUT before exiting. 23 ESEE Owner's Manual REFERENCE SECTION 24 RE-DEFINE ORIENTATION shf-F5 This command simply changes the sequence orientation arrow that is displayed to the immediate left of each line of sequence. A right facing arrow indicates that a sequence is displayed in a forward manner (i.e. 5-prime to 3-prime for nucleic acids and NH-COOH for polypeptides). The intent of this command is to allow you to enter sequences in a 3-prime to 5-prime orientation, reverse them, and have the editor understand that they are really displayed in a forward rather than reverse orientation. Please see "REVERSE" for more information how orientation affects the behavior of the editor. REMOVE NUMBERS AND SPACES alt-F2 (Processive COMMAND) All spaces and digits in the current sequence are removed processively, starting from the cursor position and ending at the end of the sequence. Walls are ignored. Please see the "SPACE" for more information on the spacing. REMOVE SPACES F2 (Processive COMMAND, AFFECTED BY WALLS) All spaces are removed from the current sequence processive, starting from the cursor position and ending either at the end of sequence or at the first wall encountered. In the case of a wall, any upstream spaces that are removed are re-inserted immediately upstream of the wall, leaving the wall's position unchanged. Another way to remove spaces is to use the REPLACE command and replace all spaces with nulls. REPLACE F9 (Processive COMMAND) This command allows you to change or delete all copies of any given character in the current sequence, starting from the cursor position and moving processively to the end of the sequence. The replace command first prompts you for the character to change and then for the character to use as the substitute. You may use the key sequence <cnt-backspace> for the WALL character as a response to the prompts.If you enter <F9> in response to the prompt for the substitute then the all downstream copies of the target character are deleted. 24 ESEE Owner's Manual REFERENCE SECTION 25 REPLICATE shf-F4 A new sequence that is a copy of the current sequence is created and inserted immediately below the current sequence. The command aborts if there is not enough computer memory to hold another sequence or if there are already 21 sequences in the editor. RESTORE shf-F9 One or more sequences are read in from a file. The specified file MUST have been created by the SAVE command. Do not attempt to RESTORE a simple ASCII sequence file, use INPUT instead. Any name, numbering, type, and orientation characteristics associated with the sequences at the time of saving will also be restored. If the editor contains only one sequence and that is empty, (eg. the initial status of the editor) the first sequence restored will become sequence #1, otherwise the restored sequences will be appended below the highest numbered sequence that already exists. The restore process will abort if there will not be enough memory to hold the restored sequences, if the restoration requires more than 21 sequences, or if there are any input/output errors. Please see SAVE for more information. REVERSE alt-F5 The current sequence is reversed, no matter what its type. This means that the last character of the sequence becomes the first, and vice versa. The reverse command reverse the direction of the orientation arrow that is displayed to the immediate left of each line of sequence. Please see RE-DEFINE ORIENTATION for more information. SLIDE LEFT [ The current sequence is pushed upstream (to the left) leaving the current position unchanged. This means that the cursor does not move relative to the screen but scrolls relative to the sequence. The sliding can only be done if there is a blank in position 1. If you need to use the character "[" then use some other rare character and then use REPLACE to change it to "[". 25 ESEE Owner's Manual REFERENCE SECTION 26 SLIDE RIGHT ] The current sequence is pushed downstream (to the right) leaving the current position unchanged. This means that the cursor does not move relative to the screen but scrolls relative to the sequence. The sliding is accomplished by inserting a blank in position 1. SLIDE RIGHT becomes inhibited when the sequence length reaches the maximum (which currently is 16,000 characters). If you need to use the character "]" then use some other rare character and then use REPLACE to change it to "]". SAVE alt-S or shf-F10 All of the sequences displayed in the editor are saved to a specially formatted file that is designed to be read with the RESTORE command. Any attributes, such as names, types, and orientations, associated with the sequences are saved as well. If the specified destination file already exists you are prompted to either overwrite it or abort the save procedure. It is strongly recommended that you use SAVE frequently so that you are protected from data loss caused by some mishap or malfunction. Input/output errors will abort the save process. Please see RESTORE for more information. SCROLL UP or DOWN ARROW When you use up (down) arrow when the cursor is on the top (bottom) line of the edit-space then the display scrolls down (up) by one group of sequences. Scrolling is not possible beyond the first (last) page. 26 ESEE Owner's Manual REFERENCE SECTION 27 SPACE IN 3 F1 (Processive COMMAND, AFFECTED BY WALLS) A space is inserted at every fourth position. This makes the sequence longer. If the sequence length reaches the maximum (16,000) then the insertion of blanks terminates with the sequence only partially spaced in triplets. All spaces are removed before the triplet spacing begins so this command could also be called "respace in 3". If a wall is encountered before the end of sequence then respacing stops at the position of the wall and everything downstream stays as it was. Triplet spacing can have a strange affect on sequences of type P. When translation is performed with P-type sequences they are spaced to be centered over the codons and thus triplet spacing is designed to keep the single- letter coded protein sequences centered over triplets of nucleic acid sequence. Use the REMOVE spaces command to get rid of spaces. SPACE IN n alt-F1 (Processive COMMAND, AFFECTED BY WALLS) This command works just like SPACE in 3 except that you are prompted to give a number for spacing. This number can be anything as long as it is less than the maximum allowable sequence length (i.e. 16,000). TAB (Processive COMMAND) The tab key inserts 10 spaces starting at the position of the cursor. If the end of sequence within 10 spaces of the cursor then action terminates at the end of sequence. You cannot use tab when the cursor is beyond the end of sequence. The TAB key is "destructive" in TYPEOVER mode, meaning that the blanks are written over any characters in the next 10 positions. This feature can be used for quick deletions because you can use REMOVE spaces to get rid of the new blanks. See SHIFT-TAB for more information. TYPEOVER Typeover mode is destructive, meaning that a typed character replaces the character at the current position rather than inserting. You cannot use TYPEOVER when the cursor is at or beyond the end of sequence. 27 ESEE Owner's Manual REFERENCE SECTION 28 TRANSLATE F4 (Processive COMMAND, AFFECTED BY WALLS) RULES for TRANSLATION: a. The current must be a sequence of type P or T. (Type T give 3-letter amino acids). b. There must be a sequence of type N somewhere above the current sequence. The first one found, moving upwards from the current sequence is considered the template sequence. c. Translation will proceed to the right (downstream) from the cursor position. d. Translation will stop when it encounters a "WALL" in the current sequence or when the end of the template sequence is reached. e. Spaces (up to the first wall) are removed from the template strand before translation. If there are any walls in the template, the translation will "jump" them, leaving a space at that position, and the translation will stay in frame. If walls are used in the template sequence then avoid having two or more walls in a row. f. If you use walls with translations, it may be a good idea to insert them (i.e, not with TYPEOVER mode) in both the template and peptide sequences. g. You may translate from with the cursor on a sequence of type N, in which case the a new sequence is created below the current sequence to hold the product. Translation this way always produces a single letter product. - Use Alt-G to see or change the current genetic code. - the product sequence will always be the same length as the template after translation UNDO cnt-U The result of any insertion, deletion, copy, join, or translation can be undone using this command provided no other key has been depressed. This includes going into windows. 28 ESEE Owner's Manual REFERENCE SECTION 29 UPPER CASE cnt-F5 (Processive COMMAND) All alphabetic characters from the cursor position to the end of sequence are converted to uppercase. The opposite action is performed by the LOWER CASE command. The editor treats upper and lower case characters as the same thing when translating, comparing or matching. The commands FIND and REPLACE, however, do make a distinction between the two cases. VERTICAL SCROLL Please see SCROLL for information. WALLS cnt-backspace (AFFECTS SPACE IN 3, SPACE IN n, TRANSLATE, AND REMOVE SPACES) Walls have three functions: Stopping the action of spacing and space removal commands, stopping translations, and acting as simple landmarks. It is a good idea to check that you are NOT IN TYPEOVER mode when putting in walls as they, as any other character, replace the character at the cursor position in that mode. AT PRINT-OUT TIME WALLS ARE NOT NUMBERED OR PRINTED. This, unfortunately may put your sequences out of alignment. Two remedies to this situation are to place a walls at the same positions in all of the sequences or to use REPLACE to remove all walls before printing (after saving your work, if you don't want to loose the wall positions). In future releases of ESEE you will be able to specify how walls are printed. WIPE alt-W or cnt-F2 Wipes all sequences from the editor. You are prompted for confirmation. The result is one empty sequence. The print-out settings are unaffected by WIPE.