What's New in Version 11.0

Initializing

Initializing GCG

New directory structure

Programs
New Programs
Unsupported Programs of this release

Enhancements
Program Enhancements

Known Issues

GCG 11.0: On all platforms

SeqWeb 3.0: All Platforms

GCG 11.0: on AIX

GCG 11.0: on Linux

GCG 11.0: on Irix

SeqWeb 3.0: on AIX

SeqWeb 3.0: on Irix

Bug Fixes

Package-Wide Bug Fixes

Initializing GCG

This is a two step process:

Step 1:

% source <path>/startup

The former “gcgstartup” has been renamed “startup”. A convenient alias “gcgstartup” is present for backwards compatibility. Note that “startup” is now present at the root of the installation.

Startup sets up the $GCGROOT environment variable, validates that the installation directories that are present and correct, adds the bin directory to the PATH environment variable, defines the “gcg” and “gcgsupport” aliases and sets up the “.wp” preferences directory if it does not exist.

Step 2:

% gcg

“gcg” is an alias that sources the “etc/aliases” file. This will display the familiar GCG banner and creates a large number of aliases. This includes the convenient aliases like “to”, “up”, “home” etc, and “noglob” versions of all of the GCG programs. (This is required so that you can use the wildcard character ‘*’ when specifying database sequences.)

New directory structure

GCG 11.0 has a significantly changed directory structure to bring it more in line with typical UNIX applications. From the installation root, the following directories are present;

· bin – the location of all the binary executable files and scripts

· doc – the html on-line help files and GCG documentation is stored here

· etc – this directory holds all the configuration files for GCG

· lib – contains the shared object libraries required by GCG programs

· sbin – contains system administration executable files and scripts

· share – contains various shared files, mostly data files for the algorithms (e.g. genetic codes, restriction enzyme files etc)

· var – contains account management, licensing and logging files.

New Programs

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The programs listed below are new to version 11.0 of Accelrys GCG (GCG).

Multiple Comparison

ClustalW+

ClustalW+ creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments. It can also plot a tree showing the clustering relationships used to create the alignment. ClustalW+ is based on version 1.83 of ClustalW, as described in Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22:4673-4680

Sequence Utilities

SeqStat+

SeqStat+ is a utility program that reads through any number of input sequences and provides some basic statistics about the files, including total length, number of sequences, and average length. Additionally it provides some extended information about the sequences depending on their type (protein or nucleotide), such as G+C% content.

SeqStat+ supports all input file formats such as BSML, FASTA, GenBank, SwissProt, and EMBL formats. SeqStat+ shall also read from STDIN as well as regular files. When a directory of files is specified as input, SeqStat+ will recursively process all files within that directory as input.

SeqManip+

SeqManip+ is a utility program that allows the user to perform some manipulations of sequences, including translation, back translation of protein sequences, splitting sequences. While individual programs to perform these tasks already exist in Wisconsin Package 10.3, SeqManip+ provides a single platform to execute all the relevant sequence operations. This saves the users from having to find and run several different applications in order to execute some basic sequence manipulations.

Database Utilities

FormatDB+

Combines any set of GCG sequences into a database that you can search with BLAST. This replaces the GCGTOBLAST program from previous software versions.

Importing and Exporting

SeqConv+

SeqConv+ is a utility program that provides batch conversions between different sequence formats. The motivation for the program is to allow an end user to easily convert between file formats to easily import data into Accelrys’ bioinformatics applications. In addition, the converter allows the user to convert our internally used formats (e.g. BSML, RSF) into formats more commonly accepted by third-party tools. The supported file formats will include BSML, GenBank, FastA, EMBL, and RSF.

Unsupported Programs of this release

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The programs listed below are available but not supported for version 11.0 of GCG.

Spew

ShiftOver

SetKeys

SeqED

Replace

OneCase

PepData

LineUp

ListFile

Lprint

GelAssemble

GelDisassemble

GelEnter

GelMerge

GelStart

GelView

GetSeq

Compress Text

ChopUp

Detab

ExtractPeptide

Red

The below mentioned programs are deprecated. The functionality of these programs has been incorporated into single program “SeqConv+”.

ToFASTA

FromEMBL

FromFASTA

FromGenBank

Program Enhancements

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Multiple Comparison

MEME +

(Multiple EM for Motif Elicitation) Finds conserved motifs in a group unaligned sequences. MEME saves these motifs as a set of profiles. You can search a database of sequences with these profiles using the MotifSearch program.

Database (Sequence) Searching

BLAST+

Searches one or more nucleic acid or protein databases for sequences similar to one or more query sequences of any type. BLAST can produce gapped alignments for the matches it finds. BLAST+ is based on version 2.2.10 of NCBI Blast.

NetBLAST+

Searches for sequences similar to a query sequence. The query and the database searched can be either peptide or nucleic acid in any combination. NetBLAST+ can search only databases maintained at the National Center for Biotechnology Information (NCBI) in Bethesda, Maryland, USA.

FastA+

Does a Pearson and Lipman search for similarity between a query sequence and a group of sequences of the same type (nucleic acid or protein). For nucleotide searches, FastA may be more sensitive than BLAST. FastA+ is based on version 3.5 of the FASTA program package (see W. R. Pearson and D. J. Lipman (1988), "Improved Tools for Biological Sequence Analysis", PNAS 85:2444-2448, and W. R. Pearson (1990).

SSearch+

Does a rigorous Smith-Waterman search for similarity between a query sequence and a group of sequences of the same type (nucleic acid or protein). This may be the most sensitive method available for similarity searches. Compared to BLAST and FastA, it can be very slow

TFastA+

Does a Pearson and Lipman search for similarity between a protein query sequence and any group of nucleotide sequences. TFastA translates the nucleotide sequences in all six reading frames before performing the comparison. It is designed to answer the question, "What implied protein sequences in a nucleotide sequence database are similar to my protein sequence?"

TFastX+

Does a Pearson and Lipman search for similarity between a protein query sequence and any group of nucleotide sequences, taking frameshifts into account. It is designed to be a replacement for TFastA, and like TFastA, it is designed to answer the question, "What implied protein sequences in a nucleotide sequence database are similar to my protein sequence?" TFastA treats each of the six reading frames of a nucleotide sequence as a separate sequence, resulting in three separate alignments for each strand. TFastX, on the other hand, compares the protein query sequence to only one translated protein per strand of the nucleotide sequence, resulting in one alignment per strand. It calculates a similarity score for alignments that takes frameshifts into account, allowing it to "join" short regions separated by frameshifts into a single long alignment. TFastX may alert you to more meaningful hits than TFastA does when the nucleotide sequences contain frameshift errors.

FastX+

Does a Pearson and Lipman search for similarity between a nucleotide query sequence and a group of protein sequences, taking frameshifts into account. FastX translates both strands of the nucleic sequence before performing the comparison. It is designed to answer the question, "What implied protein sequences in my nucleic acid
sequence are similar to sequences in a protein database?"

FindPatterns+

Identifies sequences that contain short patterns like GAATTC or YRYRYRYR. You can define the patterns ambiguously and allow mismatches. You can provide the patterns in a file or simply type them in from the terminal.

Fetch+

Copies GCG sequences or data files from the GCG database into your directory or displays them on your terminal screen.

NetFetch+

Retrieves entries from NCBI listed in a NetBLAST output file. It can also be used to retrieve entries individually by entry name or accession number. The output of NetFetch is an RSF file.

Translation

Map+

Maps a DNA sequence and displays both strands of the mapped sequence with restriction enzyme cut points above the sequence and protein translations below. Map can also create a peptide map of an amino acid sequence.

DataSet+

Creates a GCG data library from any set of sequences in GCG format. To translate nucleotide sequences into peptide sequences, include the ToProt parameter.

Protein Analysis

HTHScan+

Scans protein sequences for the presence of helix-turn-helix motifs, indicative of sequence-specific DNA-binding structures often associated with gene regulation.

SPScan+

Scans protein sequences for the presence of secretory signal peptides (SPs).

CoilScan+

Locates coiled-coil segments in protein sequences.

TransMem+

Scans for likely transmembrane helices in one or more input protein sequences.

Primer Selection

Prime+

Selects oligonucleotide primers for a template DNA sequence. The primers may be useful for the polymerase chain reaction (PCR) or for DNA sequencing. You can allow Prime to choose primers from the whole template or limit the choices to a particular set of primers listed in a file.

Known Issues

GCG 11.0: On all platforms

1. Map+: Usage of –Enzymes parameter.

In Map program, -enzyme=A* selects all the enzymes that start with ‘A’. In Map+, -enzymes=^A is the equivalent of A* (in Map) that selects all enzymes that start with ‘A’.

2. Map+ options, which are not implemented in GCG 11.0:

a.       Open (for mapping only the Open Reading Frames)

b.      Lines per page

c.       Display both forward and reverse cut positions[-BOTtom]

d.      Display enzymes cut sites in vertical mode [-VERtical]

e.       Display cut sites by vertical line [-NOCUTline]

f.        Display sequence in the output [-NOSEQline]

g.       Display Numbered scale line in the output [-NOSCALeline]

h.       Feature Character to separate each line in the map output [-FeatureChar]

3. Dataset+

a.       To avoid creating flat file databases from duplicate sequences, Wisconsin Package 10.3 database utilities supported an -exclude option, which allowed this user to specify a file containing accession numbers to exclude from loading. For data exclusion in GCG 11.0, the filename given as input to -exclude option should contain the <sequence name> to be excluded and not <accession number>.

b.      If index is set to false, .offset and .seqcat files still get created. The expected behavior is that these files should not be created. However, these files need to be present, if you would like to create indexes later.

c.       Dataset+ cannot handle sequence files having sequence name length greater than 20 characters.

d.      Special characters like hyphen ( - ) and underscore( _ ) are valid characters and can be used as part of the logical name. Other special characters like #,@,!, etc are not supported. (All GCG programs fail to read from database library containing special characters (other than hyphen and underscore) in their library logical name.)

                     For eg: globin#, globin* are not valid library logical names.

4. BLast+ program will not prompt for selection of databases. If you do not know your database choice, you must run BLAST+ service twice. Run it first with the commandline:% blast –dbreport. And then the second time specifying the database to be searched.

5. The Name program cannot be used to set new shortcuts specifying directories in 11.0. However, it can be used for the display of all the possible shortcuts supported by GCG 11.0.

6. Symbol program is used to generate new symbols that are most frequently used by the users. In GCG 11.0, Symbols cannot be used to build new symbols, instead can be used to view the Symbols existing or already set in GCG 11.0 environment.

7. NetFetch+ output file does not display the accession numbers that were fetched at the beginning of the file as in Wisconsin Package 10.3 output.

8. SRS/Lookup indices cannot be created for Refseq entries

9. PrettyBox program fails to generate a readable post script format if the input file contains more than 76 sequences.

10. Batch jobs on all new plus (+) applications fail to send an email to the corresponding user(s).

11. New plus (+) programs do not display the option "add what to command line" with -check option. In other programs, this option can be used to specify additional parameters.

12. Interactive prompts do not show begin and end range of the input sequence(s) for all new plus (+) programs. The defaults are set to 1 and -1 for begin and end range respectively.

13. New plus (+) programs cannot generate plots, charts, or other graphics

14. Plotting parameters like width and height of the graphics cannot be configured for existing programs.

15. GCG 11.0 programs are unable to read input files that are greater than 2 GB.

SeqWeb 3.0: All Platforms

1. Plus (+) programs cannot generate plots, charts, or other graphics.

2. Plotting parameters like width and height of the graphics cannot be configured for plus (+) programs and existing programs.

GCG 11.0: on AIX

1. Motifs programs terminates abruptly with an error message:

exec(): 0509-036 cannot load program <Installed Path>bin/motifs because of memory issues

2. Fasta_native programs have a limitation for large databases. The database search set should not exceed ~100,000 sequences.

GCG 11.0: on Linux

1. On RedHat 7.2, BLAST, BLAST+, and FormatDB+ does not work because NCBI BLAST version 2.2.9 is installed by default. You can extract blast-2.2.6_rh72.tgz (using the command cd $GCGROOT/bin; tar-xvzf from CDROM/lp/blast-2.2.6_rh72.tgz) library to downgrade these to 2.2.6 that work fine on RedHat 7.2.

2. Prior to building lookup indexes (gcg_srsbuild), please run unlimit, if you use csh.

3. On recent versions of RedHat Linux, if you get errors about pthread_cancel, please use your system’s versions of standard libraries. You can do this by:

cd $GCGROOT/lib/

rm -f libgcc_s.so.1

rm -f libstdc++.so.5

ln -s /lib/libgcc_s.so.1 .

ln -s /usr/lib/libstdc++.so.5 .

GCG 11.0: on Irix

1. On Irix, the following programs do not work:

·       peptidesort

·       profilescan

·       foldrna, mountains and domes

2. Following programs need more memory than other programs. For these to run, you need to set unlimit (if you use tcsh) or ulimit (if you use ksh/bash) before execution.

·       motifs

·       mfold

·       hmmerpfam

SeqWeb 3.0: on AIX

1. Motifs program fails to run when the parameter ‘Number of Mismatches’ is set to ‘2’.

2. The following programs fail to run when invoked from a SeqWeb 3.0b installation on AIX platform.

· MotifSearch program

· Profile Search program

3. After successful installation of GCG 11.0 and SeqWeb 3.0 software packages on AIX, a License check error is displayed when programs like Blast+ are invoked.

4. Run time of a Job in the Job Manager window is incorrectly displayed as 10:00:00 instead of 00:00:00 while the job is still running, but the final run time displayed after the job is completed is correct.

5. After successful installation of the SeqWeb 3.0b on AIX, the SeqWeb Administrator fails to login with the administrator User ID/Passwd. The system displays ‘Authorization required’ error message.

SeqWeb 3.0: on Irix

1. If you need to run the programs listed under GCG 11.0 on Irix, as having higher memory requirement, you need to increase the memory limits to the user under which SeqWeb 3.0 is run. Please contact your Irix system administrator about information on how to do this.

2. The following programs fail to run when invoked from a SeqWeb 3.0b installation on Irix platform.

· PeptideSort program

· ProfileScan program

3. Run time of a Job in the Job Manager window is incorrectly displayed as 10:00:00 instead of 00:00:00 while the job is still running, but the final run time displayed after the job is completed, is correct.

Package-wide bug fixes

The following bugs have been fixed in GCG 11.0.

·       In any GenBank record, the feature location was truncated if the feature has multiple lines and also the order of join and compliment are reversed while parsing the record. This has been fixed in the GCG framework in this release.

·       GCG startup script is fixed to set the plot size variables correctly for GIF and PNG drivers.

·       GCG Framework handles output files generated by programs in a different manner than in Wisconsin Package 10.3. The output files are suffixed with _1, _2 for every run of the input, so that they are not overwritten.

·       Migration scripts such as migratedbs.sh, migratepersonaldbs.sh are modified to enable the migration necessary configuration files from Wisconsin Package 10.3 version to GCG 11.0 version.

·       GCG programs failed when UniProt sequences has DOI Feature tag. This is fixed in the GCG framework.

·       GCG FastA code has been fixed for parameters such as begin and end range specification and database qualifiers at the command line.

·       Dataset program was unable to accept some of the EMBL Sequences. This has been fixed in the GCG framework.

·       SeqLab failed to display the Graphic features within the SeqLab Editor for sequences that were retrieved from SeqStore.

·       WPD (GCG 11.0 Daemon) Security has been enhanced.

·       Importing sequences into SeqLab was abruptly terminating for certain sequence records of GenBank. This has been fixed.

·       SeqLab now throws an appropriate error message when we try to load any improper list files, lacking a list file header.

·       GCG Programs now accept -def as an alias for –default.

·       SeqLab can now select and upload multiple files properly, through the “multiple file selection window”.

·       MOTIFS no longer crashes on certain prosite entries.

·       SeqMerge no longer fails to upload large SCF files through SeqLab.

·       Stdin (Standard input) could not be used with some of the Wisconsin Package programs such as Dataset. Users can now use stdin like -in=- to input data via stdin.

·       Comments tag (CC) of some EMBL-format files not read properly by GCG programs. This is fixed in the GCG framework.

·       GCG programs failed to handle sequence files with spaces in the file name. This has been fixed in the GCG framework

·       GenbanktoGCG no longer fails for sequence records that have lines greater than 86 characters.

Technical Support: support-us@accelrys.com, support-japan@accelrys.com,
or support-eu@accelrys.com

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.

What's New in Version 11.0

Table of Contents

Initializing GCG

New directory structure

New Programs

Multiple Comparison

Sequence Utilities

Database Utilities

Importing and Exporting

Unsupported Programs of this release

Program Enhancements

Multiple Comparison

Database (Sequence) Searching

Translation

Protein Analysis

Primer Selection

Known Issues

GCG 11.0: On all platforms

SeqWeb 3.0: All Platforms

GCG 11.0: on AIX

GCG 11.0: on Linux

GCG 11.0: on Irix

SeqWeb 3.0: on AIX

SeqWeb 3.0: on Irix

Package-wide bug fixes