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ESEE109E.ZIP
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ESEEHELP.FIL
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1992-06-06
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ESEE - The Eyball Sequence Editor Version 1.09e
╔═════════════════╤═══════════════════╗ ________CURSOR MOVEMENT:________
C PUT ALL seqs │ WIPE all seqs C cn-HOME...top left of page
F1 S │ DELETE a seq S F2 cn-END....bottom right of page
A SPACE in N │ REMOVE # & spaces A cn-LEFT...left 10 positions
║_SPACE in 3 _____│_REMOVE spaces_____║ cn-RIGHT..right 10 positions
C begin NUMBERING │ change NAME C cn-PgUp...first page
F3 S FILES │ REPLICATE S F4 cn-PgDn...last page
A Genetic Code │ change TYPE A cn-RET....end of sequence
║_Help____________│_TRANSLATE_________║ alt =.....go to
C UPPERcase │ LOWERcase C alt -.....WALL
F5 S Redefine ORIENT │ COMPARE S F6 [.....SLIDE Left
A REVERSE │ ║ ].....SLIDE Right
║_COMPLEMENT______│_MATCH_____________║ (Tabs are blanks in type-over mode)
║ │ ║ sh-TAB.....insert 60 spaces
F7 S PRINT │ MOVE a seq S F8 TAB.....insert 10 spaces
A JOIN seqs │ CREATE a seq A cn-A.....Advance sequence
║_BLOCK___________│_FIND string_______║ cn-E.....Extend end of sequence
C GET a sequence │ PUT a sequence C cn-U.....UNDO
F9 S RESTORE seqs │ SAVE all seqs S F10 cn-Y.....DEL to end of line
A INPUT a sequence│ OUTPUT as ASCII A cn-Z.....Del to end of sequence
║ REPLACE char │ QUIT ║ INS.....Toggle TYPEOVER mode
╚═════════════════╧═══════════════════╝ RET.....Toggle PROTECT mode
INPUT/OUTPUT Alt-F9 or Alt-i ... INPUT one raw ASCII sequence
Alt-F10 or Alt-o ... OUTPUT one raw ASCII sequence
Shf-F10 or Alt-s ... SAVE all sequences in a save file
Shf-F9 Alt-r ... RESTORE a saved file
Cnt-F1 ............. PUT ALL sequences into a database
Cnt-F9 ............ GET sequence from a database
Cnt-F10 ............ PUT current sequence into a database
Shf-F7 or Alt-p ... PRINT-OUT window
SEQUENCE Alt-F8 or Alt-c ... CREATE a sequence at cursor position
MANIPULATION Shf-F2 or Alt-d ... DELETE the sequence at cursor position
Shf-F8 or Alt-m ... MOVE the sequence at cursor position
Cnt-F2 or Alt-w ... WIPE all the sequences from the editor
Shf-F4 ............ REPLICATE the sequence at cursor position
Alt-F7 ............ JOIN a copy of a sequence onto another
Alt-F4 or Alt-t ... Change TYPE of current sequence
Alt-F6 or Alt-n ... Change NAME of current sequence
Cnt-F3 or Alt-b ... Begin NUMBERING with N
Shf-F5 ............ Redeclare Orientation
Cnt-e or Alt-e ... EXTEND end of sequence to cursor position
Cnt-a or Alt-a ... Advance sequence to cursor position
GENERAL F7 .. BLOCK (mark, copy, move, delete a block)
EDITING F8 .. FIND a string of up to 25 characters in the current sequence
F9 .. REPLACE all occurences of a given character to right of cursor
PROGRAM CONTROL
Shf-F3 or Alt-f...FILES window Alt-F3 or Alt-g...Genetic Code
Shf-F7 or Alt-p...PRINT OUT window Alt-h or F3......HELP
Alt-q or F10 or <ESC>...QUIT Cnt-U...UNDO
SEQUENCE EDITING COMMANDS
cnt-U .. UNDO
cnt-W .. Insert WALL (to block spacing and translation)
cnt-Y .. DELETE to end of line
cnt-Z .. DELETE to end of sequence
F1 .. SPACE in TRIPLETS to right from cursor position
alt-F1 .. Insert a space every nth position
F2 .. REMOVE SPACES to right from cursor position
alt-F2 .. REMOVE SPACES and digits to right
F4 .. TRANSLATE a protein sequence from cursor to right. The translation is
based upon the first nucleic acid sequence found above the protein
sequence. You can't translate beyond the end the nucleic acid sequence
F5 .. COMPLEMENT. Creates a new sequence based upon the current sequence
shf-F5 .. REVERSE the current sequence
F6 .. MATCH two sequencese. Creates a new sequence of type A if necessary
shf-F6 .. COMPARE two sequences of the same type. Creates a new sequence
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.
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.
Allow for spaces taken up by names and numbers any defined left margin,
keep this in mind! This command affects the OUTPUT command.
PAGE LENGTH: Specify the maximum number of lines to print on a page. Remember
to allow 4 lines for the title. Groups of sequences are not split over
pages. After each page a form feed is sent.
SUPPRESS FORM FEEDS: This is useful for getting two or more outputs on a page.
SUPPRESS NUMBERING: Enter the number of a sequence that shouldn't be numbered.
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 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. Enter non-
printable characters as decimals in square brackets. This string can be
added to as you go along. RET alone will clear any existing string.
Go: Starts printout. Printing is complete when the word "GO" disappears.
NAME WIDTH: You may specify any width from 0 to 64. Other values are ignored.
With a setting of 0 no names are printed otherwise the names will
be printed and the name field will be separated by the sequences by one
space.
PRINT BLANK LINES: Any print-out line that consists of blanks is normally NOT
printed. Blank lines can be forced to appear when this option is set to N,
in which case they will be printed with no numbers.
READ/SAVE print-out definition. The SAVE option allows you to save the current
print-out settings in a file that can be READ at a later time. Any valid
file name is allowed. The only option that is not saved with this command
is the list of sequences with suppressed numbering, since numbering is
really a sequence-specific attribute.
NUMBERING RULES:
By default only sequences of type N and P are numbered on print-out.
For type N: only characters in the set {A, G, C, T, U, N, R, Y} are numbered.
For type P: Only valid amino acids will be numbered.
For type T: the count on a line is based on the number of non-blank characters
divided by 3 with the remainder ignored.
For type A: all non-blank characters are numbered.