What's New in
Version 10.1
[Genhelp | Program Manual | User's Guide | Data Files | Databases | Release Notes ]
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 Accelrys GCG (GCG).
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. GCG version 10.0 shipped with NCBI's BLAST version 2.0.5. A
GCG 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 GCG, 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 section in GCG 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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| Next ]
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, GenBank
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
[ Previous | Top | Next ]
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
[ Previous | Top ]
Korn Shell Support
Problem: If you used GCG 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: GCG now correctly expands
wildcard file specifications under the Korn shell.
Limitation: If you use GCG 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.
[Genhelp | Program Manual |
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Technical Support: support-us@accelrys.com, support-japan@accelrys.com,
or support-eu@accelrys.com
Copyright (c) 1982-2005 Accelrys Inc. All
rights reserved.
Licenses and Trademarks: Discovery Studio
®, SeqLab ®, SeqWeb ®, SeqMerge ®, GCG ® and, the GCG logo
are registered trademarks of Accelrys Inc.
All other product names mentioned in this
documentation may be trademarks, and if so, are trademarks or registered
trademarks of their respective holders and are used in this documentation for
identification purposes only.
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