What's New in Version 10.1

[ Program Manual | User's Guide | Data Files | Databases ]

Table of Contents

New Program

Enhancements
Program Enhancements
SeqLab Enhancements
Package-Wide Enhancement

Bug Fixes
Program Bug Fixes
SeqLab Bug Fixes
Package-Wide Bug Fixes


New Program

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The program listed below is new to Version 10.1 of the Wisconsin Package.

Importing and Exporting

FromTrace

FromTrace converts one or more ABI or SCF trace files into GCG single sequence files or an RSF file.


Program Enhancements

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Database Searching

BLAST

Enhancement: BLAST now uses NCBI's BLAST version 2.0.10. The Wisconsin Package Version 10.0 shipped with NCBI's BLAST version 2.0.5. A Wisconsin Package patch issued in March, 1999 upgraded this to version 2.0.8.


Enhancement: The allowable range for the -WORdsize parameter has been modified. For BLASTN the range is 7 through 19. For the other BLAST programs the allowable values are 2 and 3.


FastA, FastX, TFastA, TFastX, and SSearch

Enhancement: The FastA family of programs is now based on Version 3.2t05 of William Pearson's FASTA package. (In Version 10.0 of the Wisconsin Package, the FastA programs were based on Version 3.1t12.) Because of this update, expectation values reported in a Version 10.1 FastA program's output will differ slightly from expectation values reported for the same search performed under Version 10.0.


Enhancement: The range for the -EXPect parameter has been expanded. You can now specify an expectation value as low as 0.0000000001 (10 decimal places) for any of the FastA programs.


MotifSearch

Enhancement: When you run MotifSearch with the -RSF parameter, the features in the output file are now assigned unique colors for up to 7 motifs. This change makes it easier for you to distinguish among different motifs when viewing the sequences in SeqLab.


NetBLAST

Enhancement: NetBLAST now uses the BLAST 2.0 algorithm on the NCBI server. This major update includes new parameters and a revised NetBLAST chapter in the Wisconsin Package Program Manual. Some of the new capabilities include gapped alignments, improvements to the statistics, and performance enhancements. The results generated with BLAST 2.0 can differ from those generated with the previous BLAST version supported by the server (BLAST 1.4).


Enhancement: NetBLAST has a new parameter, -PROXY. This parameter may be used to specify the host and port of a proxy server.


Enhancement: The range for the -EXPectation parameter has been expanded. You may now specify values as small as 0.000000000001 (12 decimal places) or as large as 10,000.


Enhancement: NetBLAST now issues informative error messages for many kinds of network problems.


Enhancement: The parameter -SEGments has been renamed to -ALIgnments to maintain consistency with BLAST.


Enhancement: The word "net" is now incorporated in output filenames (for example, zizm99.netblastp).


Enhancement: NetBLAST now filters the low complexity regions of query sequences by default. To suppress filtering, specify the -NOFILter parameter.


Gene Finding and Pattern Recognition

MEME

Enhancement: MEME now accepts, as input, protein sequences ending with stop codons. However, MEME fails if your input sequences contain internal stop codons.


Enhancement: The command-line summary now states that the default model is -ONEORZero.


Motifs

Enhancement: Motifs now writes an output file even when no motifs are found. Previously, the screen trace summary indicated Total finds: 0, but no output file was created.


Importing and Exporting

FromFastA

Enhancement: FromFastA can now use FastA files which have a TAB character separating the sequence name from the rest of the definition line.


Utilities

Corrupt

Enhancement: You can now run Corrupt on protein sequences as well as nucleic acid sequences.


GCGToBLAST

Enhancement: GCGToBLAST now uses NCBI's formatdb version 2.0.10.



SeqLab Enhancements

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Enhancement: The limit on the total number of queued and running jobs has been increased to 500. Previously, the limit was 50 jobs.


Enhancement: If you change your font preferences from the SeqLab Preference menu, the changes take effect immediately. You no longer have to restart SeqLab for the new fonts to be used in all of the windows.


Enhancement: When running BLAST and NetBLAST, you can now set the "Ignore hits that might occur more than how many times by chance alone" option as low as 0.0001.


Enhancement: NetFetch is no longer selected by default when you run NetBLAST.



Package-Wide Enhancements

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Translation Tables

Enhancement: Three new tables for translating the Blepharisma, Chlorophycean, and Trematode mitochondrial codes are available. For any program that supports the -TRANSlate parameter, add -TRANSlate=15, 16 or 21, respectively, to the command line to use these translation tables.



Program Bug Fixes

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Comparison

BestFit and Gap

Problem: When you ran BestFit or Gap on large sequences on some operating systems, the alignment could occasionally fail with the error message surface of comparison exceeds 5,500,000 elements.

Update: BestFit and Gap now produce alignments for large sequences on all supported platforms.


Compare and DotPlot

Known Bug: If you run DotPlot using the XWindows graphics driver with certain output files from Compare (described below), this error message displays:

*** DDClearPoints: too many points

The Xwindows graphic driver then becomes corrupted and must be restarted in order to correctly display any subsequent plots. The Compare output files causing this problem are ones that compare long sequences using a small wordsize. For example, running Compare on two sequences of length 100,000 and a wordsize of 5 reveals this problem.

Work Around: You can decrease the resolution to produce fewer points by increasing the wordsize when running Compare, or you can use a different display device for DotPlot, for example PNG or GIF.


PlotSimilarity

Problem: If you used sequences with lengths between 100,000 and 200,000 residues as input to PlotSimilarity, the tick marks on the X-axis of the output graph were not labeled.

Update: PlotSimilarity now labels the X-axis tick marks when large sequences are used.


ProfileGap

Problem: If you ran ProfileGap interactively and gave a multiple sequence specification as input, the input was rejected.

Update: ProfileGap now accepts multiple sequence inputs both interactively and from the command line.


Database Searching

Problem: If you searched a large database (one with more than 2**31 residues) using one of several database searching programs, the total number of bases searched was incorrectly reported.

Update: The counters in all database searching programs accurately report the sizes of the databases searched.


BLAST

Problem: If you used BLAST to search a large number of sequences, the search sometimes failed because it exceeded your system's memory limitations, and it reported an error message similar to:
[gcg_blastall] WARNING: Unable to open /gcgblast/est.nsq
This limitation may have prevented you from specifying, for example, GenEMBL and EST in a single search.

Update: The memory management of the BLAST program is improved, enabling you to search larger data sets.


Known Bug: In some cases when you run BLAST and specify multiple databases for the search set, the search fails or only some of the databases are searched.

Work Around: If your BLAST search fails or if not all of the databases are searched, rerun the search including the full paths in your database specifications. Note that databases located in the current working directory or the directory associated with the logical name BLASTDir may be specified without full paths.


Problem: If you searched multiple databases, the summary information shown at the bottom of the BLAST report incorrectly reported only the number of sequences in the first database.

Update: The summary information now reflects the actual number of sequences in all searched databases.


Problem: (IRIX 6.5 or later only) When you ran BLAST with the value of -PROCessors set to a number greater than one, the program halted with the error message:
[gcg_blastall] ERROR: Unable to open thread.

Update: The current version of BLAST supports multi-threading on all IRIX platforms.


Problem: If you ran BLAST on more than one database when using the -BAtch parameter, the search would only run on one of the databases.

Update: BLAST now searches all specified databases when -BATch is used.


Known Bug: If you want to search multiple databases using BLAST in batch mode, you must use the -INfile2 parameter in front of the database names. For example:
% blast query.pep -INfile2=pir,swplus -BATch


Problem: If you ran BLAST with the -BATch parameter and specified a single database on the command line, the search failed if you did not precede the database name with the -INfile2 parameter.

Update: You can now specify the database name without the -INfile2 parameter.


Problem: If you ran BLAST with the -BATCH parameter, some of the parameters that you specified interactively may not have been properly written to the init file, causing the search to fail.

Update: All parameters are properly written to the init file, and the search runs successfully.


Problem: (For all BLAST programs except BLASTN) If you performed a search with unacceptable values for either -GAPweight or -LENgthweight parameters, your output simply read No hits found , but there were no other error messages and the search was not performed.

Update: BLAST now produces informative error messages if you specify inappropriate gap penalties.


Known Bug: If you specify inappropriate gap penalties for a BLASTN search, the program uses default penalties.


Problem: If you mistakenly tried to run BLAST with the -TBLASTX parameter when using a protein query or protein database, the program crashed.

Update: BLAST now identifies this error and exits with an error message.


Problem: The divider line at the start of the list portion of a BLAST output file had an extra blank space following the ".." terminator.

Update: The extra space is no longer present.


Problem: If there were any uppercase letters in the name of a query sequence that originated from a database (for example ba:ECOLAC) the output filename consisted of both uppercase and lowercase letters (for example ECOLAC.blastn).

Update: Now only lowercase letters are used to compose output filenames.


FastA, FastX, TFastA, TFAstX, SSearch, and FrameSearch

Problem: (Solaris only) When using one of the multi-threaded database searching programs (FastA family of programs and FrameSearch), you could never access more than two processors, even if your computer had more than two processors available and you used the -PROCessors parameter to specify more than two processors.

Update: The multi-threaded database searching programs now can use more than two processors on all operating systems.


FastA, FastX, TFastA, TFastX, and SSearch

Problem: When you searched a database with one of the FastA programs, the list file did not contain the Begin or End attributes for the segment of the database sequence that matched the query sequence.

Update: The list file output for the FastA programs now contains the Begin and End attributes for the matching region of the database sequence.


Known Bug: The FastA programs use a large amount of memory and the amount of memory needed increases as the number of processors used increases. This memory requirement can cause the programs to terminate with an error when you run them using more than one processor.

Work Around: Use the unlimit command to increase the amount of memory you can use. If this doesn't help, reduce the value of the -PROCessors parameter.


Known Bug: (Solaris 2.6 or 7 only) If you start one of the FastA programs, then convert it into a background process by using Ctrl-Z and the bg command, the program hangs or terminates prematurely with an error.

Work Around: To run one of the FastA programs in the background, add -Default and & to the command line or alternatively, run the program on the batch queue by including the -BATch parameter on the command line.


Known Bug: When you perform a database search with one of the FastA programs and produce a protein-protein alignment using the BLOSUM50 scoring matrix, the sequence symbol X is treated as a partial match to the symbol T.


FastX and TFastX

Problem: In the display of the alignments, the numbering for the translated query sequence was supposed to be in accordance with the original nucleotide sequence. The numbering of the first amino acid corresponded to that of its nucleotide codon. However, the numbering was incorrect for any amino acid other than the first one.

Update: The numbering of the translated query sequence now corresponds to the numbering of the original nucleotide sequence.


FastX

Problem: If you ran FastX with the -MARKx=10 parameter, the al_start, al_stop, and al_display_start coordinates for the query sequence were incorrect in the parsable output file.

Update: The coordinates for the query sequence in the FastX parsable output file are now correct.


Problem: If you ran two FastX searches that differed only by the value of the -PROCessors parameter, you might see a difference in the two outputs for the percent identity reported for the same sequence match.

Update: The percent identity calculation no longer varies with differing values of the -PROCessors parameter.


TFastA

Problem: In the display of the alignments, the numbering of the bases corresponding to the displayed translation of the database sequence was incorrect when the match occurred in the middle of the database sequence.

Update: The alignment numbering is now correct.


SSearch

Problem: Under Histogram Key in the SSearch output file, the description for the z-score computation is mislabeled. The z-scores are actually computed from the Smith-Waterman scores.

Update: The SSearch output now always reads z-scores computed from s-w scores.


FindPatterns

Known Bug: FindPatterns cannot use patterns consisting of an "OR" specification followed by a repeat count that matches with a count of zero. For example, the following pattern fails to match "gc":
g(a,t){0,2}c

Work Around: Separate the alternative subpatterns into new patterns. In the above example, this would result in the following two patterns:
ga{0,2)c
gt{0,2)c


LookUp

Problem: If you used LookUp to search a sequence database and requested fragments output, LookUp displayed a syntax error if it encountered a feature containing an accession number that had a version number appended to it (for example, join(M34058.1:1612. .1703, [...]).

Update: LookUp can now process accession numbers that contain version numbers.


Problem: If you ran LookUp on FastA-format databases using the parameter -SHOrtest=x, LookUp acted as though you had used -SHOrtest=x+60.

Update: LookUp's -SHOrtest parameter now functions properly with FastA-format databases.


Motifs

Problem: If you ran Motifs with the -RSF parameter, not all of the motifs found would be annotated as features in the RSF file.

Update: All of the motifs now appear as features.


NetBLAST

Known Bug: If you specify an inappropriate value for either the -GAPweight or -LENgthweight parameter, NetBLAST uses default values for both penalties.

Work Around: Consult the NetBLAST documentation for valid gap penalties.


Problem: You could not turn off the screen trace to NetBLAST.

Update: You can now use the parameters -MONitor and -NOMONitor to turn on or off the screen trace.


Problem: If you specified -TBLASTX without also specifying -DBNucleotideonly, NetBLAST did not prevent you from a choosing a protein database. This could result in a BLASTX search rather than the intended TBLASTX search.

Update: If you now use -TBLASTX you cannot search a protein database, even if you omit the -DBNucleotideonly parameter.


Problem: If you specified both -TBLASTX and -DBProteinonly, NetBLAST would preform a BLASTX, rather than a TBLASTX search.

Update: Now if you specify both -TBLASTX and -DBProteinonly, NetBLAST terminates with an informative error message.


Problem: It was not obvious that you could run NetBLAST searches as batch jobs since the documentation did not include the -BATch parameter.

Update: The NetBLAST documentation now describes the -BATch parameter.


NetFetch

Problem: In some cases, if you ran NetFetch using the -TOP parameter, NetFetch tried to retrieve all the sequences in the NetBLAST input file.

Update: NetFetch now tries to retrieve only the number of sequences specified by the -TOP parameter.


ProfileSearch

Known Bug: (Tru64 UNIX only) Searches of nucleotide databases can fail due to a floating-point overflow during the normalization step.

Work Around: Use MotifSearch to search nucleotide databases. In general, GCG does not recommend using ProfileSearch to search nucleotide databases. However, including the -NONORmalize parameter causes ProfileSearch to skip the normalization step, and your search completes successfully.


StringSearch

Problem: On some platforms, if you ran StringSearch with the -BATch parameter, the search string was distorted, and the search did not return the desired results.

Update: StringSearch now runs correctly in batch mode on all platforms.


Evolution

PAUPSearch and PAUPDisplay

Problem: When you specified an output file name that included a GCG logical name, PAUPSearch and PAUPDisplay did not expand the logical name to its full UNIX path specification and did not write the output file in the intended location.

Update: PAUPSearch and PAUPDisplay now expand all logical names to their full UNIX path names.


PAUPDisplay

Problem: If you ran PAUPDisplay to reroot a large tree, occasionally PAUPDisplay would output the message "ReadString error" and would claim that there were no trees in the file.

Update: PAUPDisplay can now reroot large trees.


Problem: PAUPDisplay could not read a .pauptrees file that contained a large, deeply nested tree. It would terminate prematurely with a "treeEltStack overflow" error message.

Update: PAUPDisplay can now read and display larger trees.


PAUPSearch

Known Bug: If you try to find trees with PAUPSearch using the exhaustive search method with distance as the optimality criterion, the search terminates prematurely with an out of memory error message.

Work Around: Use a search method other than exhaustive search or an optimality criterion other than distance.


Problem: PAUPSearch displays the bootstrap tree (labeled with the bootstrap percentages) and the bootstrap partition table to the screen, but does not write the information in the .pauptrees output file. You had to include the -LOGFile parameter to save this information in an output file.

Update: When you perform a bootstrap analysis, PAUPSearch now automatically writes the bootstrap information to a .pauplog file that has the same base name as the .pauptrees file.


Problem: If you had a large number of sequences (and thus a large phylogenetic tree), PAUPSearch would sometimes put a line break in the middle of a tree number or tree length when it wrote the .trees file. PAUPDisplay could not read this corrupted file and would terminate with an error.

Update: PAUPSearch now puts line breaks in appropriate places in the .trees file output.


Known Bug: If you run PAUPSearch on sequences whose names contain both a hyphen and an underscore, the resulting output cannot be read by PAUPDisplay.

Work Around: When creating sequences for use by PAUPSearch, choose names that do not contain both a hyphen and an underscore.


Gene Finding and Pattern Recognition

MEME

Problem: If you ran MEME and requested more motifs than actually exist in the input sequences, on rare occasions some of the profiles in the output file were populated completely with zeros.

Update: MEME now reports only valid profiles.


Problem: If you gave as input to MEME a sequence specification that included a wildcard, but resolved to only a single sequence, the proposed profile output name included the wildcard as well.

Update: MEME now proposes a valid output filename without any wildcards.


Editing and Publication

PrettyBox

Problem: If you ran PrettyBox on a set of sequences that were not padded to the same length, instead of being padded with blanks, the shorter sequences would be padded with the characters from the start of the next sequence.

Update: PrettyBox now correctly displays sequences of different lengths.


Problem: PrettyBox did not show the last character of the consensus sequence.

Update: PrettyBox now shows all characters of the consensus sequence.


Nucleic Acid Secondary Structure

StemLoop

Problem: If you ran StemLoop on a sequence that had a loop of only one base, that base might not be displayed.

Update: StemLoop now displays singleton loops of a stem-loop structure.


Importing and Exporting

FromGenBank

Problem: If you ran FromGenBank on an entry with more than 50,000 lines of annotation, FromGenBank would fail with an error message.

Update: FromGenBank can now convert a GenBank sequence with an arbitrary number of annotation lines into GCG format.


Problem: If you specified a directory with the -DIRectory parameter, FromGenBank ignored this parameter and wrote the results to the current directory.

Update: FromGenBank now writes the results to the directory you specify with the -DIRectory parameter.


ToFastA

Problem: If you ran ToFastA with the -Default parameter, the program summary was written to your terminal.

Update: Now when you run ToFastA with the -Default parameter, ToFastA does not generate a screen trace unless you also specify the -SUMmary parameter.


Printing and Plotting Utilities

LPrint

Problem: In some cases, the -COLumn parameter for LPrint did not have any effect.

Update: LPrint is now consistent with the documentation. When you use -COLumn with a value between 40 and 255, this value determines the number of characters per line unless reading from standard input. When reading from standard input, LPrint uses a value of 80 by default. If you use -LANdscape on the command line and read from standard input, LPrint uses a value of 132.


Utilities

DataSet

Problem: GCG flat file databases are limited to .seq and .ref files of size 2 gigabytes or less. If the .seq or .ref file generated by DataSet exceeded 2 gigabytes, the database created was unusable, but no error message was issued.

Update: DataSet now fails with an error message when either the .seq or .ref file exceeds the 2 gigabyte limit.


GCGToBLAST

Problem: If you ran GCGToBlast on peptide sequences with embedded stop characters (*), GCGToBLAST removed the characters before formatting the sequences for use with BLAST.

Update: GCGToBLAST no longer removes embedded stop characters from sequences.


Reformat

Problem: If you ran Reformat, using as input a file whose name had consecutive periods (for example, my..seq), this name was copied directly into the header of the reformated sequence, and GCG programs were unable to read the file properly.

Update: Reformat now inserts a space between the periods, and GCG programs can read the file successfully.



SeqLab Bug Fixes

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Editor Mode

Problem: If you loaded a sequence with more than 100 features into the Editor, SeqLab could stop working.

Update: SeqLab can now handle sequences that have more than 100 features.


Problem: If you selected a region of a sequence, then moved the cursor using a repeat count, SeqLab did not always highlight the cursor position.

Update: SeqLab now highlights the appropriate base if you move the cursor after highlighting a region.


Known Bug: To append or delete characters at the end of a sequence, you move the cursor to the right of the sequence end. When editing the longest sequence in the Editor, the cursor is not visible at this position.

Work Around: Type a tilde (~) while the cursor is positioned at the end of the sequence. This action inserts two end-gap characters and provides a visible cursor location from which you can edit.


Problem: If you used the Copy function from the Editor and then attempted to paste into another window, SeqLab sometimes unexpectedly terminated. The paste operation could be in SeqLab itself or any other window on your monitor.

Update: Using the Copy function from the SeqLab Editor will not have any effect on subsequent paste operations in other windows.


Trace Viewer

Problem: SeqLab could not load 8-bit compressed SCF trace files into the Trace Viewer.

Update: SeqLab can now properly read 8-bit compressed SCF files.


Problem: The Trace Viewer sometimes wrote error messages to your terminal complaining about illegal values in its scroll bars.

Update: The Trace Viewer now manages its scroll bars correctly.


Problem: If you loaded a trace file, then ran a program that inserted gaps in the sequence, the Trace Viewer showed incorrect association of the trace peaks with the sequence characters.

Update: Inserting gaps does not change the associations of trace peaks with sequence characters.


Problem: If you loaded a sequence into the Editor and its trace in the Trace Viewer, then used a repeat count to move the cursor in the Editor, the cursor would move in the Editor, but not in the Trace Viewer.

Update: All cursor movements in the Editor are reflected in the Trace Viewer.


Problem: In some circumstances, when you used the Editor's Copy function to copy a sequence that had associated trace data, SeqLab terminated unexpectedly.

Update: The Copy function now works correctly when copying sequences that have associated trace data.


Problem: If you rearranged the order of sequences in the Editor and those sequences had associated trace data, the Trace Viewer would sometimes associate a sequence with another's trace data.

Update: Rearranging sequences will no longer cause improper associations of trace data.


Programs Run Through SeqLab

Known Bug: If you run a program that generates an RSF file as output when an RSF file with the same name is listed in the Output Manager and you try to add the new file to the SeqLab Editor, the old file is sometimes added.

Work Around: Rename or delete the previous RSF output file before any subsequent runs of the program.


Known Bug: If you select an aligned group as sequences in the Editor and use them as input to a program that produces RSF output, the alignment in the RSF output file could be distorted.

Work Around: In the rare circumstance that you use an alignment as input to a program producing RSF output, carefully check the alignment in the output file to ensure none of the sequences are padded erroneously with leading gaps.


Database Searching

BLAST

Problem: The default values for the "Maximum number of sequence listed in the output" and "Display alignments from how many sequences" options did not agree with the corresponding command-line defaults.

Update: The default value for the "Maximum number of sequence listed in the output" option has been increased to 500. The default value for the "Display alignments from how many sequences" option has been increased to 250; its maximum allowable value has been increased to 500. These default values are consistent with the command-line defaults.


Problem: The label for the filtering option read "Filter input sequence for low complexity/repeat regions," even though BLAST can only filter low complexity regions, not repeats.

Update: The label for this option now reads "Filter input sequences for low complexity regions."


Problem: When you selected the "Process the output to be a valid GCG list file" option, the output was in fact the unmodified NCBI BLAST2 output.

Update: The label for this option now reads "Generate output in native format."


Problem: If you ran BLAST and chose to generate output in native NCBI BLAST2 format, it was possible to add the output file to the Editor or the Main List from the Output Manager, despite the fact that the file was not a valid list file.

Update: SeqLab will no longer add a native BLAST output file to the Editor or Main List.


StringSearch

Problem: Sometimes when you ran StringSearch, SeqLab stopped working. This problem happened when the Job Manager received longer lines of output than it could handle.

Update: SeqLab now trims long lines to reasonable lengths for the purpose of displaying screen trace information in the Job Manager, and StringSearch will complete.


WordSearch

Problem: The label for the "Simplify sequences before comparison" option was unreadable until the option was selected.

Update: This label is now readable regardless of whether or not the option is selected.


Evolution

PAUPDisplay

Known Bug: If you are trying to display a maximum likelihood tree and you click the "gamma distribution" radio button to set "Distribution of Substitution Rates Across Sites," and then click "estimated by program" under "Set shape parameter to," this latter radio button group becomes improperly grayed out, implying that you cannot change "Set shape parameter" back to "specified below."

Work Around: If you click a second time on the "gamma distribution" radio button, the radio buttons under "Set shape parameter to" become active once again.


PAUPSearch

Problem: The "When to Collapse Zero-length Branches to Yield Polytomies" option was set to "never" by default when it should have been set to "if maximum branch length = 0."

Update: PAUPSearch now uses the correct default setting for the "When to Collapse Zero-length Branches to Yield Polytomies" option.


Gene Finding and Pattern Recognition

CodonPreference

Problem: To specify the density of a plot, you gave a value for the "Number of bases per 100 platen units" option, but the units for this value are bases per centimeter.

Update: The label for this option now reads "Number of bases per centimeter."


FindPatterns

Problem: The option "Show patterns composed of six or more symbols" did not have any effect on the FindPatterns output.

Update: This option has been removed.


MEME

Problem: In the options window for MEME, if you selected the "Search both strands" option, only one strand was searched.

Update: Now when you select the "Search both strands" option, both strands are searched.


Mapping

Map, MapPlot, MapSort, and PeptideMap

Problem: If you selected the "Minimum site length" option, it appeared that the default value of 6 was chosen, but this value was not used unless you clicked on the associated slider.

Update: The default minimum site length is now 1, and you must explicitly change it in order to use another value.


Problem: The label for the "Minimum site length" option was unreadable until the option was selected.

Update: This label is now readable regardless of whether or not the option is selected.


Printing and Graphics

Problem: When you printed an alignment to a PostScript file, certain PostScript viewers had difficulties displaying more than the first page.

Update: Multi-page PostScript files created by SeqLab can be displayed by any PostScript viewer.


Problem: If you printed an alignment from the SeqLab Editor with a large scale factor selected (e.g. 128:1), SeqLab would sometimes hang indefinitely.

Update: SeqLab now prints alignments with any scale setting.


Problem: If you printed graphics to a PNG output file, you could only print to a file with the default filename.

Update: SeqLab now uses any filename you specify for printing graphics in PNG format.


Other

Problem: After long sessions that involved many Save operations, SeqLab sometimes terminated unexpectedly.

Update: SeqLab now functions reliably when you are performing many Save operations during a session.


Problem: If your .datasetrc file contained more than 50 entries, SeqLab would terminate unexpectedly.

Update: If SeqLab encounters more than 100 entries in your .datasetrc file, it prints a warning message but does not terminate.


Problem: On rare occasions, the SeqLab initialization procedure hung indefinitely and the SeqLab window never displayed.

Update: The SeqLab initialization procedure now completes and the SeqLab window displays.


Problem: If SeqLab displayed a dialog window requiring you to make some choice and, instead, you closed the window by clicking on the "X" in the upper right corner, SeqLab sometimes entered an unstable state.

Update: The Close function for this type of dialog is now disabled, forcing you to make a choice.


Problem: The Save As... button in the Output Manager sometimes created a copy of the file instead of renaming it.

Update: The Save As... button now always renames the selected file.


Problem: On some X servers, the SeqLab Editor used a proportionally-spaced font instead of a fixed-width font, which resulted in gaps appearing in the text display. This problem was seen when you selected the font named "application" in the Editor but could have occured in other situations as well.

Update: SeqLab now only accepts fixed-width fonts in the Editor.


Known Bug: Programs like StringSearch that can generate large amounts of screen trace output to the Job Manager can overload SeqLab. In such cases, the program continues to run but the Job Manager at some point stops displaying the screen trace. The running job continues normally and runs to completion.


Known Bug: The Save Settings button does not work for external programs. It only works for GCG programs.


Problem: If you modified the range of an entry displayed in the Main List and clicked "Create As New Entry," SeqLab displayed a prompt asking if you wanted to modify an entry that is in a nested list, even if the entry was not in a nested list.

Update: SeqLab now displays this prompt only when appropriate.



Package-Wide Bug Fixes

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Korn Shell Support

Problem: If you used the Wisconsin Package under the Korn shell, wildcard file specifications on the command line were not expanded properly. For example, if you used FastA to search a set of sequences specified as *.seq, only the first sequence was searched.

Update: The Wisconsin Package now correctly expands wildcard file specifications under the Korn shell.


Limitation: If you use the Wisconsin Package under the Korn shell, you may not use GCG command aliases in UNIX multi-command pipes. If you want to write a command-line pipe, you must either specify the command by the path to the executable file or you must redefine the alias, disabling wildcard expansion.


RSF Files

Known Bug: An alignment contained in an RSF file may be distorted in the rare circumstance that you use that RSF file as input to a program that produces RSF output.

Work Around: Do not use an RSF file containing an alignment as input to Reformat -RSF. If you use an RSF alignment as input to a program producing RSF output, carefully check the alignment in the output file to ensure none of the sequences are padded erroneously with leading gaps.


Problem: If an RSF file contained one or more sequences with a comment line that started with the word "name," you could not refer to some of the sequences in the file by name.

Update: The word "name" at the start of a comment line no longer corrupts an RSF file.




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