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DNA Translator Stack Version .96+ Copyright 1990,1991 D. J. Eernisse usergdef@ub.umich.cc.edu or usergdef@umichub.bitnet Submitted to IuBio Archives 11/21/90 .96.1 See end of this file for most recent changes Made a few changes made possible by HC 2.0 ask file and answer file commands, and a new ufFile function in the stack script. This made possible the replacement of filename() and newfilename() XFCNs. Changed "Extract Gene" script slightly for the gene mapping background to guide the user more completely to the right string file. Changed "Export Interleave File" script for the utilities background button "N-str" so that the user doesn't have to wait for the calculation of match characters before naming an export file. Removed the "Show Dialogue" XCMD which was not being used. Removed reference to it in help text .96.2 Uploaded to account gdef 11/23/90 Expanded the 12 amino acid fields slightly under the lower codon usage graph, because they were not displaying all three letters on some cards. This problem must have happened with conversion to HC 2.0. Smith, et al. 1990, in press now has complete citation. Added a few more icons for taxon picker button. Updated help text to indicate that the stack is now available on the EMBL file server by sending the command: GET MAC_SOFTWARE:DNATRANSLATOR.HQX to NETSERV@EMBL.BITNET The stack is also now available at iubio.bio.indiana.edu [Note: This site has since changed to ftp.bio.indiana.edu] ftp ftp.bio.indiana.edu user: anonymous pass: (any) cd [archive.molbio.mac] get dnastack.hqx .97 Uploaded to account and to iubio.bio.indiana.edu 12/17/90 Added "Navigator" to menu for utility cards for no good reason except that it was very easy to do in HyperCard 2.0. Now "Normal Menu" only appears in the File menu of utility and gene order cards if a small screen Mac is being used. Changed help files slightly to reflect some bitnet users' problems with downloading the stack from my account. Instead of 'get gdef/dnastack' try 'get gdef:dnastack' or 'cd gdef' and 'get dnastack'. Added "Replace Data", "Create New Card" and "Export Data" features to gene order card(s). Now it is generally easier to add gene order cards. Made it possible to customize the "Taxa" menu in additional gene order cards, if they are added. See script for "Taxa" menu button. Also updated documentation somewhat with instructions on the import/export of codon usage and gene order data. Improved the editor on the utility cards, and removed the "Turn on Editor" menu option under "Edit". Changed "OpenStack" script to always show the brief introduction on the title card when the stack is first opened. Fixed a minor glitch that kept imported GenBank and EMBL files from exporting to a file as string sequences (although the strings appeared in the N-str field properly). Added Miyamoto, et al. 1990 to reference list. Fixed some other minor glitches introduced recently for interleave export. Simplified N-in, N-out, P-in, and P-out menus somewhat. Added pop-up menu to PAUP/MacClade file save button. Added auto-stripping of linefeeds on most imports of text. Added an auto-pathsetting feature for the extraction of gene sequences and saving them to files on the gene order card. .97.1 12/23/90 (Posted to account about 12/27/90) Added visual cues to make the pull-down menus more obvious on the utility cards. Updated the HierPopUp XFCN by Jon Pugh to version 2.5, just posted. This may improve compatibility on some Macs. .97.2 1/10/91 (Posted 1/11/91) Used a different approach to nucleotide to peptide translation that sped translation up considerably. Now there is an option of formatted (original slow) or string (faster) translation. Added the Xlate and editScript XFCNs by Nigel Perry (not used yet). .97.3 1/13/91 (Not posted) Improved sequence importing on the utility cards, especially for importing string sequence files from disk. Now there are the options of replacing or appending present strings in the N-in or P-in fields, and imported strings can be user-specified subsequences of the original string file. There is also an improved dialogue interface for importing/exporting sequences or multiple aligned sequences. 1/20/91 (Not posted) Fixed minor problem on animated organism picker button on card 1. .97.4 1/22/91 (Not posted) Changed script for exporting interleaved sequence so that dots are added to the end of any sequence shorter than the longest sequence interleaved, to compensate for "left-over" nucleotides or peptides, should they occur. .97.5 1/30/91 (Not posted) Added four custom XFCNs and associated scripts and resources, courtesy Nigel Perry from London, England. These have enabled an order of magnitude improvement in the translation facility! This version is still in transition as Nigel is still modifying his XFCNs. .97.6 2/6/91 (Posted to account 2/7/91) Nigel Perry has again written several new XFCNs, but until these are received and implemented, I have updated the stack mostly to fix two bugs. One bug occurred with EuGene -> Nexus formats with more than 9 aligned sequences. The other bug was for the new (faster) EuGene -> Nexus conversion, which gave an incorrect value for the number of characters. I have also added an auto-numbering field to the utility cards to help keep track of which card is which. I also made the newer (faster) conversion routines automatic rather than optional. .97.7 2/10/91 (not posted) Improved the sequence speaker, which now works fine with the newer systems since it no longer requires MacinTalk. The new speaker is capable of speaking a little faster and sounds better. There are now menu options for controlling the automatic speaking speed and volume. Now it is also possible to optionally speak the sequence as it is entered, either via the Edit menu or by clicking on the new Speaker button revealed when the Edit field expands. For now, only nucleotides are spoken with the new speaker. Also put together a small stack (Sequence Speaker) which only has the speaking function, with options for nucleotides, peptides, or all letters and numbers, as well as volume and speed control knobs and import/export options. This stack uses methods similar to the new ones above but, unlike the DNA Translator stack, it has 'snd' resources for all letters and numbers, not just 'a,c,g,t,u & n'. Because the 'snd' resources are large, about 3K each, peptide speaking has not yet been implemented in DNA Translator, except by the older method. In the near future, I expect to add this capability with more compact snd resources. The new stack, which is about 150 K, is also available for anyone who wants it, with the same copyright restrictions as DNA Translator. .97.8 2/14/91 (not posted) Added the option of exporting extracted sequences on a Gene Mapping card directly to any Utility Card, with or without retaining the sequence on the Gene Mapping card. Fixed a minor problem with the selection of a taxon on the Utility Card which tended to empty the taxon selection, requiring reselection. The chicken (GGAMTCG) mtDNA sequence was downloaded from the most current version of EMBL and is now available. Added a few recent references to the reference list as well. Improved the selection of the preferred "text creator" for the export of text to one's favorite word processor, on both Gene Mapping and Utility cards. The script should be a little faster and shouldn't add to the free space (i.e., size) of the stack. .97.9 2/24/91 (posted) This is a major but provisional upgrade, because it is the first version to feature several new XFCNs by Nigel Perry, as well as our reworking of the menus on the Utility cards. The old menus have not been completely replaced, however, because Nigel is still trying to get hierarchical menus to work. There is presently considerable redundancy in the scripting on the Utilities cards. I have moved the sound controls to under the Editor field and moved the reformat command to the Editor menu. 2/27/91 Fixed minor problem with scripts ('SetVol' to 'SetVolume' in bg btn Volume on Utilities cards; 'Send mouseUp to bg btn reformat' to 'reformat' on Utilities cards' bg script). 3/3/91 Removed the need for the user to select a sequence file when a sequence is extracted by clicking on a gene map button (with Command Key depressed or via the Extract menu). The file is now accessed automatically unless it is not found. Fixed field button which hides the fields on the utility cards, which I broke when I added the sound controls. Also fixed the lock button. To save on stack size, I removed old handlers and menu buttons that have been replaced. This reduced stack size by about 30K but might have led to errors if any scripts still refer to those handlers or bg buttons. 3/6/91 Wrote a new script so that it is possible to extract all available sequences for any gene button clicked on a Gene Mapping card, not just the sequence for the taxon of the displayed gene map clicked on. This option is available either by clicking on the gene button with both the CommandKey and ShiftKey depressed, or by selecting 'All Taxa' after clicking on the 'Extract' menu button. At present, this will automatically export the coding sequences of all nine MTCG sequences to a Utility Card that a user selects through a dialog box. Rewrote the conversion of Nexus to Hennig86 or Phylip formats. The conversion is much faster now. Also discovered a problem with the strDelta xfcn, although it may still be ok the way it is used at other places in the stack. 3/10/91 Rewrote the codon data import scripts to conserve space and speed import and recalculation of 12 new taxa for graph displays. Also wrote scripts to export codon preference files in Wisconsin GCG format. Right now this is supported only if a user holds the option key down when clicking on a taxon in the scrolling list on the title card (the same one used for selecting 12 taxa). The stack will also convert GCG format data files to the spreadsheet format that I use. Again, for now this is only supported if one holds the option key down when clicking on the graph icon (1) from the title card. I used this conversion to incorporate data for about 50 additional species, mostly nuclear plus a couple of chloroplast codon usage tables. These were all downloaded via anonymous ftp to sites at Harvard, Indiana and Switzerland (all pretty much the same files, mostly produced by Michael Cherry). To save space, I combined taxa when I could, and report average values (not compensated for different amounts of available sequence data per species, e.g., human vs. sheep, although this would be easy to do with spreadsheet formulas). Made several major changes to economize on stack space. The stack no longer has a mitochondrial DNA emphasis, except for the gene maps. Full names for the species added above have been entered. 3/28/91 Changed the nucleotide -> peptide string translator to support ambiguous nucleotide symbols recommended by the IUPAC-IUB Biochemical Commission. Now, depending on the codon usage table selected, if a codon (e.g., ATR) is translated only if the translation is unambiguous; otherwise the codon is translated to "?". Also added option of stopping at termination codons. 4/1/91 Changed menu interface on Gene Mapping and Utility cards. I now use HyperCard 2.0 menus exclusively, which meant that I had to make major changes to these background scripts. All commands and icons are now accessible to users of Macs with small screens. There are also a variety of minor improvements to scripts. The addition of the Resources and XScrollBox XFCNs now permit more streamlined menus, such as when a user selects a codon usage table for translating nucleotides, or chooses a gene, etc. A script handler (addTable) for adding or deleting a custom codon usage table has been added, but the XFCN used does not seem to be working right for adding a table. As soon as this XFCN problem is resolved, these options will be added to the Utility Card menu. .98 4/1/91 (uploaded to account) .98.1 4/3/91 (uploaded to account) Fixed minor bug that incorrectly hid the new Gene Mapping menus on small screen Macs only. Added "Interleave File" to N-str menu on Utility cards. This allows the interleaving of a disk file to large to import into the N-str field. It is likely that add this capability more generally to several conversion routines in the near future. Removed two temporary SSU rRNA conversion routines. .98.2 4/8/91 (uploaded to account) Fixed minor bug that was introduced in .98.1 that broke the N-str or P-str contents interleave conversion ("Interleave File" worked). Added ShowDialog 1.4 XCMD and about 10 new custom menus, now all of which are fully implemented yet. Added Convert menu to Utilities Cards, and the more general capability of going from an input disk file to an output disk file in most cases (the others will be modified soon) so that files larger than 30K can be converted. Moved most of the menu commands to the stack background, so that all cards now have custom HyperCard 2.0 menus. Fixed the Codon Usage Table creator/deletor. Removed the redundant codon usage tables. Now this facility is available from the Edit menu. Added "Backtranslate" capabilities (which uses the new NucleoXlate XFCN by Nigel Perry). This allows pep- to nucleotide translations, incorporating conventional ambiguous nucleotide codes. Any codon usage table may be used. Replaced Resources() XFCN with Available() XFCN, by Nigel Perry, from his soon-to-be-released Pictoids 1.1 (update of Regions 1.0). .98.3 4/13/91 (Uploaded to account) Completely reworked string input/output scripts, including support in the main Convert Menu. Now the 30K maximum size of a field is not a limitation for either import or export. Rewrote nucleotide to peptide formatted translation script. It is now quite a bit faster, but still not as fast as it should be. Removed "Extract Reading Frame" options, which are unnecessary with the fast string translations. I have experienced a troublesome problem with System crashes when certain actions are executed from the Convert menu. I have been unable to find the problem, and everytime I think I have a repeatable crash- generating sequence, the problem goes away. Since the crashes never occur when the same actions are selected from the "field" pulldown menus (e.g., N-str and RFs), I suspect the problem has something to do with sending mouseDown messages from a handler called by the menumsg "DoConvert" in the Utilities background script. The crash is a fairly ugly one, which leads to diagonal lines across the screen and requiring turning off the power switch, but doesn't seem to corrupt the script. If anyone can predictable duplicate this crash, please contact me. Added a "Trim Sequences" option for nucleotide strings. This will trim a specific number of sites from the left side of every string sequence, or else trim from the right side starting at a particular site. I have found it useful in doing manual alignments with a text editor such as QUED. [Now called "Manual Interleave"] .98.4 4/16/91 (uploaded to account) Fixed the crashing problem above (I think) by replacing the use of the translit XFCN with the replace XFCN in certain instances in the bg btn scripts, N-str and RFs. I'm still not sure why these crashes occur, but the debugger allowed pinpointing the offending command. Added automatic taxon look-up for Nexus and Phylip.result formatted aligned sequence text that is being converted to string or Nexus output formats. These might lead to problems if a nonstandard Nexus or Phylip.result file is to be converted, but they save the hassle of trying to remember the name of the first and last taxon names. This feature was formerly available for EuGene input files, but hasn't yet been implemented for interleaved files. .98.5 4/27/91 (uploaded to account) Fixed more events of the crashing problem above. I think I got them all this time. Also, many misc. bugs and problems were fixed, both on utility cards and gene mapping cards. Added two mtDNA gene maps, one for a yeast species and one for a ciliate species. The introns and other differences from animal mtDNAs required some modifications to the scripts. The yeast, but not the ciliate, MTCG sequence will be distributed with the stack at this point. The ciliate sequence can be obtained from EMBL (MIPAGEN) and converted to a string sequence on a utility card (It should be named PauMTCG and placed in the MTCG Sequences folder, which should be kept in the same folder as DNA Translator). I will likely add Podspora anserina mtDNA and liverwort and tobacco cpDNA gene maps in the near future, but will not distribute the string sequences because each > 100,000 bp. In order to deal with extraction of subsequences from string sequence files that are > 30K, such as PauMTCG, I have rewritten the extract script so that the entire starting sequence is not imported to a field. The multiple extract script has not been modified yet, however. .98.6 5/1/91 (not uploaded) Added support for conversion of CLUSTAL output files of multiple aligned sequences -> Nexus, PHYLIP, Hennig86, string sequence formats. Taxon lookup is automatic. This works with all the nucleotide and peptide sample files that I have available (which isn't very many). Modified the Nexus peptide export so user has a choice of Standard or Mammal mtDNA codon translated cost matrices (PROTPARS) or none at all. Added a major feature for extracting features from a documented GenBank or EMBL sequence file. Now, in addition to extracting a continuous string sequence from such a file (as before), a user can optionally also construct a comma-delineated matrix which can be directly used to make a new gene mapping card. Once an output matrix is produced, it can be imported when "New Card" is selected from the "Edit" menu on a Gene Mapping card. This will automatically produce a "smart" gene map which has the same coordinate system as the documented sequence. Alternatively, the matrix can be sorted or customized in a spreadsheet program such as Excel (select comma-delineated text import). This conversion routine does not presently produce multiple sequence maps on the same card, all with the same starting origin, but it would be easy enough to combine matrices and adjust coordinates in Excel, using the animal mtDNA matrix as an example. I call it a "smart" gene map because it can automatically zoom in on any region at any scale, and can extract the sequence for any region CommandKey- clicked on, or selected from a scrolling list of features. How general this GenBank/EMBL conversion routine is remains to be seen. It works on various sequence files that I have on hand, which show a range of format styles themselves. I have provided an option to edit the full feature names and abbreviations during import, or you can let the script do it automatically and make any needed changes in Excel. .98.7 Fixed inconsistencies in converted GenBank/EMBL files. Added idleCursor XCMD from Nigel Perry for PAUP and MacClade buttons. Added a FastConvert for EMBL/GenBank sequence extraction. This seems to work fine, subject to possible memory limitations. I used it on a molecule of 157K bp without incident. Now, reading the file into memory takes much longer than the conversion. FastConvert requires either the EMBL "//" sequence end delineator or no characters, other than white space, following the initial sequence. Changed speaker to be ready for letter resources, if the user adds them. Only A,C,G,T,U & N are presently supported, but all other letters and numbers are available in the freeware stack on my account, Sequence Speaker, available by anonymous ftp to 'um.cc.umich.edu' then type 'cd legd' and 'get SeqSpeak' (about 120K compressed I think). Each snd resource is about 3K, so adding these snd resources with ResCopy for peptide speaking will add about 80K to the stack. Added set userLevel and Volume commands to stack script. Made updates to help file. Added three cpDNA map matrices to Sample Data folder. Import the individual files or a simplified, 3-taxon matrix (available soon), by selecting "New Card" from the "Edit" menu of a Gene Map card. Note that adding a matrix with a full list of features will add roughly 50 K to the stack. .98.8 5/5/91 (uploaded to account) Fixed several problems with autozoom on gene maps and a few problems with the EMBL import. Added a gene map for 3 green plant cpDNAs, with only genes which were in common to 2 or more included in the matrix. The 3 molecules start with their normal coordinate system. Added automatic scale bar to gene maps. Fixed misc. other problems. .98.9 5/9/91 (uploaded 5/15/91) Added an "Add Sequences" operation, using the new addNucleotide() XFCN by Nigel Perry. Also added an explanation of what it and "Trim" do to the help documentation. [Now called "Combine Sequences"] .99 5/20/91 (uploaded to account) Added CommandKey equivalents to many of the menu items. Change the sequence extraction on the gene mapping cards to permit selecting a gene and taxon from scrolling list. The old extract routine is now called "Click Extract". Uncovered a problem that may have prevented the multiple sequence extraction from working in the last few posted versions. Added features to the "Trim" function, so that, given an input set of strings or a single interleave block, it is now possible to extract a subblock of aligned sequences as the second of three interleave blocks in the output. For example, with 50 strings of length 2000, you can "trim" the strings into interleaves that go from 1 to 250, 251 to 269, and 270 to 2000, by specifying 251 and 269 after "Custom" selection of the first coordinate (1 by default). Even better, you can output the block 251 to 269 directly to Intelligenetics format, which is acceptable input for the RNA folding program MulFold. (You will probably want to strip the gaps before importing to MulFold.) See documentation for more details. .99.1 5/22/91 (uploaded to account) Fixed a recently added problem which disrupted the formatted reading frame output. Added the Fold() XFCN by Nigel Perry which should speed up some operations such as interleave and translations to formatted reading frames. Changed some of the CommandKey equivalents. Added a CODONPREFERENCE output, but it doesn't appear to be working correctly. I was attempting to output just the 'p' statistic which the UWGCG manual discusses. The average value of 'p' should be highest for encoding frames, and it is not. This is still experimental. .99.2 5/24/91 (uploaded to account) Fixed a problem with the codon cards that kept the coding for menu selected genome (top graphs) from updating properly when moved to a new card. Also changed the titles for the graphs and made other changes to several scripts. Replaced "***" and "End" with "TER" in present data matrix, although "***" referred to no evidence for coding (0 % usage). This affected MtMouse and MtRat, especially. Added "Print Codon Cards" to the "File" menu. Fixed a problem with "Zoom" on gene mapping cards. Now when "Both" is selected when a user wishes to center both gene maps on a particular gene, both maps are centered properly, not just the top one. Disabled "CodonPreference" added in .99.1. The results of this function are better than they were in .99.1 but there is still a problem ('p' values are too high, I think). To enable it for testing see the RFs button script. I also added Sum() XFCN for this purpose (see stack script for credits). 5/29/91 Added support for GeneJockey sequence files. This would only be useful if someone needs to extract a sequence from a file saved in GeneJockey format. It make require a bit of editing if the sequence is preceded by much documentation. Refixed the problem discussed in .97.6 update that led to problems with EuGene reports that had more than 9 taxa. Apparently, the earlier fix was somehow eliminated. Moved the PAUP and MacClade buttons up because the idleCursor sometimes interfered with text scrolling. This "feature" is easily disabled in the button script (see script comments) if so desired. 5/31/91 Fixed a minor problem introduced when GeneJockey support was added that disabled the GenBank/EMBL import feature. Made a menu option for changing the taxon label or gene button fonts, which is useful for choosing between optimal printing of the gene maps and viewing them on screen. 6/2/91 Discovered that the Insect mtDNA code was somehow substituted for the Bacterial code, which should be "standard". The full matrix was correct, so this problem must have been entered when I last made a reduced matrix for import to the stack. There is another problem, which I will check out when I import a corrected matrix. I also added Bacillus to the full codon usage matrix, thus 'Bacteria' now includes Bacillus. Added a report button to the Codon card upper graph. By clicking this button, a report for each amino acid's codon family and each codon's percentage use is generated, for the taxon/organelle combination currently selected for the upper graph. Discovered a minor problem with the reformat command in the editor field (Utility cards). I'm not sure when this was introduced (or when the field got checked 'Don't Wrap') because it used to work. Fixed a problem with importing Nexus files from the pull-down N-out or P-out menus. .99.3 6/3/91 (Uploaded 6/4/91) The problem referred to on 6/2/91 was investigated. Due to a minor problem with a script, some codons were duplicated when codon families were calculated. About 1 in 5 taxa had 1 or 2 duplicated codons (1 that was incorrect). Also fixed other problems associated with importing a new codon matrix (including some temporary bypasses I left in the last time I imported). Added the option of exporting a codon family report for all taxa, not just the currently selected one. Added support for import or export of FASTP format sequence files, to make CLUSTAL easier to use. So far the conversion of FASTP to string sequence formats must be done through the pull-down menus under the N-str or P-str fields, while exports can also be done via the main Convert menu. Fixed an apparent problem with interleaving peptide strings from the Convert menu. Improved card printing capabilities of Gene Mapping and Codon cards. Fonts automatically adjust to "Times" or "Palatino" postscript fonts during printing (If your LaserWriter doesn't have "Palatino", adjust the script of bg btn "TaxonA" on a Gene Mapping card. There is also an option to only print the gene maps, surrounded by a border, not the rest of the card or navigation buttons. .99.3a 6/6/91 (not uploaded) Fixed the PIR-formatted sequence to string sequence conversion (same problem as discussed 5/31/91). Also discovered that the findinfield() XFCN fails to find text after about the first 30K of a variable. This truncated multiple sequence conversions that had a sequence start after 30K into the file. I modified the script to get around this limitation, so now files with lots of GenBank, EMBL, or PIR sequences should all be converted, not just the first 30K or so. This was tested with about 40 PIR-formatted sequences in a single text file. .99.3b 6/11/91 (not uploaded) Added a "Composition" output option for string nucleotides. This exports a comma-delineated table of values of length, base composition, gaps, and AT(U)/GC content, for each string sequence. Finally got around to changing the "Anticodon" pulldown menu on the codon usage cards to support the "standard" code of 1 anticodon per codon. The menu and contents of the anticodon field are now automatically adjusted when the currently selected taxon in the top graph is changed from mitochondrial to nuclear or chloroplast, or the reverse. The mtDNA anticodons are based primarily on mammalian mtDNA (22 different tRNAs/anticodons) so these shouldn't be relied on for, say, yeast mtDNA. For the standard code, nonsense codons are given a corresponding anticodon, even if one doesn't exist. .99.4 6/19/91 (not uploaded but submitted along with manuscript to CABIOS) Added a "Filter IUPAC-IUB" option to replace ambiguous codes in string sequences with "N" or whatever character a user enters. This was added because EuGene apparently does not support these codes. Actually, all characters ≠ {A,C,G,T,U,N} are replaced. Added a "Tally Autapomorphies" function which converts nucleotide strings to strings of "•", "-" or " " where "•" are autapomorphies for each sequence, " " are "?" or "N" and "-" is everything else. This yields a graphic presentation of how divergent each sequence is, but only relative to the next most divergent sequence in the set of strings analyzed. It is also useful for catching regions of an alignment that can be improved or replaced with "?" for single taxa, but again won't help if 2 or more taxa are off in their alignment but well aligned with each other. A tally is computed for each sequence as (N1/N2) where N1 = autapomorphies and N2 = total sites (nucleotides plus gaps but not missing data). [Now called "Tally Unique Sites"] .99.4a 6/25/91 (not uploaded) Added a "ACGTU" to "01233" function to convert nucleotide strings to Hennig86-style number coding. As for the Nexus to Hennig86 conversion, gaps can be specified as 5th base ("4") or as missing ("?"), and all nongap (".") characters not in {A,C,G,T,U} are converted to "?". This is much faster than the Nexus to Hennig86 conversion and the output can be interleaved as for any other set of strings. .99.5 6/29/91 (uploaded 7/15/91) Added support for new features (versions ≥ .99.4) via the Convert menu, so that large sequence files can be managed. Adjusted the "Tally Autapomorphies" feature to compensate for a peculiarity discovered in the translit XCMD. Revised help file somewhat. [Now called "Tally Unique Sites"] .99.6 8/14/91 (not uploaded) Some minor changes have been made in the course of using the stack for a large rRNA project. Upgraded translit XCMD with new bug-fix version (see .99.5). .99.6a 8/23/91 (uploaded) Improved cpDNA map data substantially, due to help from Dr. Ken Wolfe at Indiana University. See references online for more details. The cpDNA string sequences are not provided with the stack, but can be obtained upon request or by converting the GenBank/EMBL sequences via the nucleotide string conversion facility. The sequences should be named, MpoCPCG, OsaCPCG, and NtaCPCG and placed in the "Sequences" folder. .99.7 9/8/91 (uploaded 9/15/91) Changed interface of utility cards to make them hopefully easier for first time users. The View menu now permits hiding of the 'Menu Buttons' except for the general navigation buttons, the 'Field Menus' beneath the edit fields, and the 'Edit Fields' themselves. None of these are essential as most conversions are now provided by the main menus, and the card has a less cluttered appearance without them. A new help feature and corresponding question mark icon were added. When clicked on, the icon becomes hilited, the 'Field Menus' are hidden, and a help field becomes active. Then, whenever the cursor is over an object such as a field or button, some accompanying explanatory text is displayed. The only problem with this is that the free space in the stack immediately increases by about 130K as soon as help text is displayed. This could cause problems if a user did not have extra space on their disk, but otherwise should be autocompacted when the stack is closed. Users familiar with the stack will probably want to leave this help facility turned off. Updated online help. Corrected the cost matrices for DNA/RNA to coincide with Albert et al., in Press (also publications of Farris, Felsenstein). These are not added at present but can be viewed from the View menu. .99.8 9/23/91 [uploaded to account, also to ftp.bio.indiana.edu] Wrote a new stack (in three days!) called Aligner, for manual alignment of multiple string sequences (DNA Translator or simple format). This was inspired by Ralph Gonzalez' nifty stack called MultiDNA but is much more powerful than that stack. Aligner will be incorporated into the DNA Translator package, which it was designed to complement, and will also be distributed separately. The version number will be kept the same as DNA Translator for convenience sake. .99.9 9/29/91 [uploaded to account] Added a "Gene Browser" optional function for the gene mapper cards. This displays the gene name of gene buttons while the cursor is on top of them. Before, when the button was too narrow to display the name, it was necessary either to click on the button or to zoom in on that gene region. The "View" menu has been updated to reflect the new function, including remembering whether to turn gene browsing off or on, depending on the last user selection. .99.9a 9/30/91 [uploaded to account] Uncovered and fixed a few minor problems with the gene mapping background scripts. Changed references to "FASTP" to "FASTA", the more current version of this program. Rewrote parts of help file (more rewriting is still required). Renamed several of the functions in the dialog boxes of the Convert menu. Aligner stack also revised. 1.0 10/3/91 [uploaded] Intelligenetics, simple string (one sequence per line, no names or spaces) and FASTA formats can now be converted to DNA Translator string format output. These are supported from "String Nucleotides" in the Convert menu, or from the pull-down N-str menu. FASTA conversion was previously supported but only from the N-str menu. 1.0.0a 10/7/91 [uploaded] Fixed a few problems with sequence extraction on the gene mapping card background. One was introduced in vers. .99.9a. Another kept "Extract" from working when only one sequence was available. 1.0.0b 10/8/91 [uploaded] Discovered and fixed a problem with exporting codon usage data. Changed taxon names used in codon usage graphs to plural when they represent averages for more than one species.