SRS 8.1 file updates
Updates of SRS files since the release of SRS8.1
This page lists file updates for the folowing SRS8.1 distribution directories:- icarus/db (flatfile/xml parsers, .i .it files)
- icarus/lion/emboss (emboss definition files)
- srstags/srstags/web/views (jsp views)
Updates are also available by ftp (login required) from downloads.biowisdomsrs.com, directory parser/srs81 The updated files are also available as tarball: srs81updates.latest.tar.gz
We also provide a tarball just containing the files which have been updated upto a certain date: srs81updates.DATE.tar.gz from: http://downloads.biowisdomsrs.com/parser/srs81 For detail on the updates available in these tarballs, see the corresponding README.srs81updates.DATE file in that same directory
See README.updates for general information on how to update your SRS installation
There is an rss feed where SRS81 parser updates are announced the moment they are available: http://downloads.biowisdomsrs.com/parser/rss/srsparser81.xml We also announce updates via a mailing list (Important fixes inmediately, small fixes/improvements are usually announced when we make a new srs81updates.DATE.tar.gz file. To subscribe to this mailing list please contact srs_support @ biowisdom.com
| Date | Database | File | Description |
| 2008/08/22 | emboss | icarus/lion/emboss/remap.i icarus/lion/emboss/showalignn.i icarus/lion/emboss/showalignp.i | Fix so showalign and remap will correctly use the colors specified by the user to color sequence regions |
| 2008/08/18 | reactome | icarus/db/reactome.i icarus/db/reactome_schema.i | Changes for release 25 of the reactome database. Note that we have changed the database name as used in the interaction with mysql to Reactome |
| 2008/08/07 | system uniprot ipi | icarus/db/srsgen.i icarus/db/swisscommon.i icarus/db/swissprot.is icarus/db/uniprot.i srstags/srstags/web/views/swissentry/swissentry.jsp | Changes to handle the new format of the DE lines in uniprot. We have added new fields: Name, AltName,Contains, Includes and Flag, but have kept the old Description field in order to query the entire contents of the DE lines. We also added a new synonym finder which uses the Name and AltName fields. Note that the new srsgen.i file needs to be merged with your copy of that file in SRSSITE |
| 2008/08/04 | enzyme | icarus/db/enzyme.i icarus/db/enzyme.is icarus/db/enzyme.it srstags/srstags/web/views/enzymeentry/enzymeentry.jsp | removed the disease (reference to omim) field, as it is no longer used |
| 2008/07/29 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcore_schema.i | Changes for release 50 of ensembl |
| 2008/07/29 | uniprot ipi | icarus/db/swissprot.is icarus/db/uniprot_swissprot.i icarus/db/uniprot_trembl.i | Changes needed to make sure we correctly link to the enzyme database with the new format of the uniprot description line. You may have to rebuild the links between uniprot_swissprot/trembl and enzyme after applying this update |
| 2008/07/29 | system | icarus/db/dbxref.i icarus/db/href.i | Changes to allow for the new references to BindingDB in uniprot. Please note that you will need to merge href.i and dbxref.i with your copies of these files in SRSSITE |
| 2008/07/28 | iprmatches | icarus/db/iprmatches.is | fix for links to prodom entries in iprmatches |
| 2008/07/02 | kegg | icarus/db/ldrug.i icarus/db/ldrug.is srstags/srstags/web/views/ldrugentry/ldrugentry.jsp | Added support for the new Source and Component fields in the kegg drugs database (ldrug) |
| 2008/07/02 | chebi | icarus/db/chebi_schema.i | Update for small chebi schema change in release 46 |
| 2008/06/24 | genecards | icarus/db/genecards.i icarus/db/genecards.is srstags/srstags/web/views/genecardsentry/genecardsentry.jsp | Change to allow for teh mew MilliPore references in GeneCards |
| 2008/06/12 | system | icarus/db/dbxref.i icarus/db/href.i | Added support for the new hogenom and hovergen hypertext links in uniprot |
| 2008/06/09 | kegg | icarus/db/lenzyme.is | fix for a problem with hypertext links from lenzyme to lcompound |
| 2008/06/02 | embl genbank | icarus/db/emblrelease.i icarus/db/genbankrelease.i | Change needed to cope with the increasing sizes of EMBLRELEASE, GENBANKRELEASE and DDBJRELEASE. After applying this update you will have to re-index the primary accession number (pac) field. It is important that you apply this change before you install the next (June 2008) full releases of these databases, as otherwise you will not be able to access all entries |
| 2008/06/02 | kegg | icarus/db/pathway.is | Fixed a parsing issue with the description line in some entries |
| 2008/05/27 | system | icarus/db/dbxref.i | Change needed to handle the new links to the Candidia Genome Database in uniprot. Please merge the changed dbxref.i file with your copy in SRSSITE |
| 2008/05/14 | system | icarus/db/ftseq.is | Correction for coding error which would break sequence feature retrieval |
| 2008/05/13 | fasta | icarus/db/fasta.is | Change needed to handle some cases of output from fasta3.5 |
| 2008/05/13 | blast | icarus/db/blastn.i icarus/db/blastp.i icarus/db/blastx.i icarus/db/tblastn.i icarus/db/tblastx.i | Change to make sure blast honours a user request to use ungapped aligments |
| 2008/05/12 | kegg system | icarus/db/kegggenome.i icarus/db/kegggenome.is icarus/db/srsgen.i srstags/srstags/web/views/kegggenomeentry/kegggenomeentry.jsp | Added support for the new ANNOTATION line in kegggenome. Note that you will have to merge the new srsgen.i file with your copy of this file in SRSSITE |
| 2008/05/12 | kegg | icarus/db/kegg_species.i | latest update for kegg species mapping file |
| 2008/05/07 | genbank embl refseq system | icarus/db/gbemblcommon.is icarus/db/href.i | Added special handling for Korean patent numbers when including a hypertext link to the European patent Office. Note that the new version of href.i needs to be merged with your copy of this file in SRSSITE |
| 2008/05/06 | system | icarus/db/dbxref.i icarus/db/href.i | Added support for the new nmpdr link in uniprot |
| 2008/04/29 | system | icarus/db/ftseq.is | Change needed to handle a change in the way unknown gaps are specified in EMBL/GenBank/DDBJ Feature tables and contig construction representations |
| 2008/04/17 | genecards system | icarus/db/genecards.i icarus/db/genecards.is icarus/db/href.i srstags/srstags/web/views/genecardsentry/genecardsentry.jsp | Updates for version 2.38 of genecards |
| 2008/04/01 | fasta | icarus/db/fasta.is | Changes needed to handle output from fasta 3.5. Our fasta parser should now be able to handle output generated by fasta 3.3, 3.4 and 3.5 |
| 2008/03/26 | system | icarus/db/dbxref.i icarus/db/href.i | Added support for the new ProMEX hypertext link in uniprot. Note that you will have to merge the new versions of href.i and dbxref.i with your copies in SRSSITE |
| 2008/03/20 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcore_schema.i | Changes for ensembl release 49 |
| 2008/03/18 | chebi | icarus/db/chebidatamodel.i | Fixes for a few hypertext link problems in chebi entry display |
| 2008/03/14 | chebi | icarus/db/chebi.i icarus/db/chebi_schema.i icarus/db/chebidatamodel.i srstags/srstags/web/views/chebientry/chebientry.jsp | Changes for release 42 of chebi. A mass and charge field have been added |
| 2008/03/13 | genecards | icarus/db/genecards.is | Change so we do not include the synomyn origin (EG/HGNC) in the synonym index |
| 2008/03/05 | genbank refseq medline | icarus/db/genbankcommon.i icarus/db/medlinecommon.i | Changes needed to handle the increasing growth of several indices in EMBL, GenBank and Medline. Applying these changes requires re-indexing and will cause major disruption. Please read instructions in http://downloads.biowisdomsrs.com/parser/srs81/UPDATE.20080503 before applying these updates |
| 2008/02/29 | system | icarus/db/dbxref.i icarus/db/href.i | Added support for the new 2d-ecoli and phosphosite hypertext references. Note that you will need to merge the new versions of dbxref.i and href.i with your copies of these files in SRSSITE |
| 2008/02/21 | emboss | icarus/lion/emboss/sixpack.is | fix to prevent sixpack indexing to hang on an empty results file, which in some cases can bring down an SRS server |
| 2008/02/14 | medline | icarus/db/medlinecommon.i | The 2008 release of medline has 16880015 entries, which is about 100000 more than can be accomodated by the 3 byte id space we allocate by default for a database. The result is that for the final 100000 entries in medlinerelease, wrong entries (from the beginning of the database are returned). The updated medlinecommon.i file will correct this, allocating 4 bytes for entry identifiers. Note that you must re-index both medlinerelease and medlinenew for this to take effect. Note that after applying this update, and while re-indexing is in progress, the old indices will still be working, so there is no need to take medline offline (unless you are concerned about those 100000 wrong entries) |
| 2008/02/07 | system | icarus/db/dbxref.i icarus/db/href.i | Added support for the new world-2dpage link in uniprot |
| 2008/02/01 | uniprot ipi | icarus/db/swissprot.is | Change to make sure that we can still extract the EC number from the uniprot description line after the description line structure changes announced for late February (see http://beta.uniprot.org/docs/sp_soon.htm). The new structure should not cause problems for the current handling of the description line in SRS, but once the data in the new format is available, we will provide additional changes to take advantage of the new structure |
| 2008/01/25 | system | icarus/db/dbxref.i icarus/db/href.i | Added support for the new pdbsum and vectorbase links in Uniprot. Please note that the new href.i and dbxref.i files need to be merged with your copies of these files in SRSSITE |
| 2008/01/18 | emboss | icarus/lion/emboss/tmap.i icarus/lion/packages/emboss.ip | Changed the TMAP tool (EMBOSS) to take alignments as input. Note that if you have already installed EMBOSS, you have to change the association of TMAP from sequence data input to alignment data input. This is easiest done by editing SRSSITE/packChanges.i, and change "PROTSEQ_DATA.applications.app:$TMAP_APP" to "PROTALI_DATA.applications.app:$TMAP_APP". |
| 2008/01/18 | kegg | icarus/db/pathway.is | Fixes for some issues with image maps when multiple pathway images are displayed |
| 2008/01/17 | system genbank embl refseq | icarus/db/dbxref.i icarus/db/gbemblcommon.is icarus/db/href.i | Added hypertext links for imgt/gene-db dbxrefs, and suppressed hypertext links for imgt/lims from refseq, as the values currently used in refseq do not provide a usefull way for linking. Note that you will need to merge the new versions of dbxref.i and href.i with your versions of these files in SRSSITE |
| 2008/01/17 | kegg | icarus/db/pathway.is | Fix to remove the duplicate display of map numbers |
| 2008/01/03 | geneseq | icarus/db/aageneseqtar.it icarus/db/nageneseqtar.it | Change to make sure prisma will download geneseq tar files, even if the size of the file has not changed |
| 2008/01/02 | pdbfinder | icarus/db/pdbfinder.i icarus/db/pdbfinder.is srstags/srstags/web/views/pdbfinderentry/pdbfindersequence.jsp | Added support for the new compound lines in the chains subsections. Note that after this update you will have to index the new chaincompound field. |
| 2007/12/14 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i | Update for release 48 of ensembl |
| 2007/12/11 | kegg | icarus/db/kegggenome.it | fix to make sure that prisma has permission to unpack the kegggenome tarball |
| 2007/11/29 | kegg | icarus/db/kegggenes.is | Fix for an error in an earlier update, whch caused some indices to remain empty. After applying this fix please re-index kegggenes_na and kegggenes_aa, and rebuild the links to these databases |
| 2007/11/14 | kegg | icarus/db/kegg_species.i icarus/db/kegggenes.i icarus/db/kegggenes.is icarus/db/kegggenes_aa.i icarus/db/kegggenes_na.i icarus/db/lcommon.is icarus/db/lenzyme.is | Added support for the new structure field in kegggenes, fixed a minor parsing problem for lenzyme, and updated the kegg species mapping file |
| 2007/11/08 | genecards system | icarus/db/genecards.i icarus/db/genecards.is icarus/db/href.i srstags/srstags/web/views/genecardsentry/genecardsentry.jsp | Added a product/service section to the entry display, which includes the new Genetex lines and Abcam lines. Also allow for the new DiscoverX line, but this is not yet used in the entry display. Note that you will have to merge the new href.i file with your copy in SRSSITE |
| 2007/11/06 | cath | icarus/db/cath.i icarus/db/cath.is | Change needed to handle case sensitive ID values in cath. Note that we now use the extended cath code as primary identifier |
| 2007/11/06 | entrezgene | icarus/db/entrezgene.is | Change to allow for hypertext links to uniprot in the reference sequence section of the entry display |
| 2007/11/05 | reactome | icarus/db/reactome.i | Added missing field definition |
| 2007/11/05 | cath | icarus/db/cath.i icarus/db/cath.is icarus/db/cath.it srstags/srstags/web/views/cathentry/cathhierarchy.jsp | Changes to make sure the latest version of cath is downloaded by prisma, and a parser correction for version 3.1 |
| 2007/11/01 | reactome | icarus/db/reactome.i icarus/db/reactome_schema.i | update for reactome version 22, and corrections for various link definitions |
| 2007/10/31 | system uniprot | icarus/db/dbxref.i icarus/db/uniprot.i icarus/db/uniprot_swissprot.i icarus/db/uniprot_trembl.i | Added support for the new refseq link in uniprot, including an indexed link between uniprot and refseqp (which will have to be build after applying this update). Note that the new dbxref.i file needs to be merged with your copy of this file in SRSSITE |
| 2007/10/30 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensemblcommon.i icarus/db/ensemblcore_schema.i icarus/db/ensemblproteinmodel.i | Updates for ensembl release 49, and some improvements for the display of the protein for ensembl transcripts |
| 2007/10/09 | uniprot ipi | icarus/db/swissprot.is | Removed some debugging code in hypertext link generation |
| 2007/10/08 | system uniprot ipi | icarus/db/href.i icarus/db/swissprot.is | Updated hypertext links for HGNC database |
| 2007/09/27 | chebi | icarus/db/chebi_schema.i | Schema update for Chebi release 37. There are no major changes |
| 2007/09/25 | genbank refseq | icarus/db/genbank.is | Correction for an error in the creation date production |
| 2007/09/24 | system | icarus/db/srsgen.i | Added BL2SEQ to DNASEQ_DATA and PROTSEQ_DATA so BL2SEQ appears in the applications drop down menu |
| 2007/09/17 | genbank refseq | icarus/db/genbank.is | Change needed to generate an entry creation date for entries which do not have a submission date |
| 2007/09/14 | genbank refseq | icarus/db/genbankcommon.i | Fix for a problem which could cause the references to be printed twice when looking at a text entry |
| 2007/09/10 | pdbfinder | icarus/db/pdbfinder.it | Added explanation of the ATOM and SEQRES fields |
| 2007/09/07 | embl genbank refseq system | icarus/db/emblcommon.i icarus/db/emblnew.i icarus/db/emblnewfiles.it icarus/db/emblrelease.i icarus/db/gbemblcommon.is icarus/db/general.it | Changes for release 92 of EMBL. These include a number of new fields for all databases in EMBL format: FtStart and FtEnd can be used to query for features with start/end in a give range, FtRange can be used to find features which overlap with a range. We also added a field for EcNumber, DbXref and Locustag in the feature table. Applying these changes will cause disruption, as the new fields need to be indexed. We suggest you apply these changes with the next full update of EMBL, due soon. Also make sure your srsgen.i file is up to date |
| 2007/09/05 | genbank embl refseq | icarus/db/gbemblcommon.is | Fix for indexing problems for the ftrange field for single nucleotide features, and inproved the hypertext link from refseqp to refseq via the coded_by feature qualifier |
| 2007/09/05 | refseq | icarus/db/refseqnew.i icarus/db/refseqrelease.i | Reduced the chunksize for indexing, as some file containing large chromosomal entries are starting to require more memory |
| 2007/09/03 | genbank refseq | icarus/db/genbank.is | Added credate token, needed for indexing the creation date field in genbank/refseq |
| 2007/08/30 | transfac | icarus/db/tffactor.is | Minor fix for sequence comment html link |
| 2007/08/23 | geneseq | icarus/db/geneseq.is | Added a space between consecutive GO identifiers to improve web display |
| 2007/08/23 | geneseq | icarus/db/aageneseq.i icarus/db/geneseq.is icarus/db/nageneseq.i | Added support for additional external DB links |
| 2007/08/21 | genbank embl refseq system | icarus/db/gbemblcommon.i icarus/db/gbemblcommon.is icarus/db/genbank.is icarus/db/genbankcommon.i icarus/db/general.it icarus/db/srsgen.i | Added a number of new fields to the sequence features for data in genbank format: FtStart and FtEnd can be used to query for features with start/end in a give range, FtRange can be used to find features which overlap with a range. We also added a field for EcNumber and LocusTag in the features tables, and expanded the data fields to provide both submission and latest udpate dates. Applying these changes will cause disruption, as the new fields need to be indexed, and we suggest you apply this change with the next release of genbank. Note that the new copy of srsgen.i needs to be merged with your copy in SRSSITE |
| 2007/08/21 | clustalw | icarus/db/clustalwcommon.i | Changed srs 8.2 value to valStr for Iterative option |
| 2007/08/21 | entrezgene | icarus/db/entrezgene.is | Correction for a change in the entrezgene data: the Gene source id has moved to a different xml tag |
| 2007/08/21 | clustalw | icarus/db/clustalw.i icarus/db/nclustalw.i | Fix to remove multiple line breaks that shouldn't be present |
| 2007/08/20 | unigene | icarus/db/unigene.i | Removed links definition for SwissProt databases, added definition for UNIPROT virtual database |
| 2007/08/20 | go_xml | icarus/db/go.it | Updated GO ftp location to point ftp.geneontology.org |
| 2007/08/16 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcore_schema.i | Some minor changes for ensembl version 46 |
| 2007/08/15 | embl | icarus/db/emblnew.it icarus/db/emblnewfiles.it | Change to make sure prisma also picks up deleted annotated contigs |
| 2007/08/14 | pdb | icarus/db/pdb.i icarus/db/pdb.is srstags/srstags/web/views/pdbentry/pdbentry.jsp srstags/srstags/web/views/pdbentry/pdbmodres.jsp | Added support for the MODRES fields in the Entry view |
| 2007/08/14 | pdb | icarus/db/pdb.is | Added translation for 2 letter na codes so sequence appears in views |
| 2007/08/13 | ensembl_mysql | srstags/srstags/web/views/ensemblproteinentry/proteinrefs.jsp | Correct formatting for non-named protein domain list feature table |
| 2007/08/10 | pdb | icarus/db/pdb.is | Added support for multiple entries in SPRSDE line |
| 2007/08/09 | clustalw | icarus/db/clustalw.i icarus/db/clustalwcommon.i icarus/db/nclustalw.i | Added support for clustalw2. Uncomment ClustalIter_Option and relevant command in apllication files to enable. Ensure location and name of clustalw program is correct |
| 2007/08/03 | genbank refseq | icarus/db/genbank.is | Correction for an error when indexing the ECnumber and molecular weight field |
| 2007/08/03 | pdb | icarus/db/pdbmodel.it | Correction for the searchname used by prisma for pdbmodel on the download site |
| 2007/08/01 | embl genbank genecards interpro medline refseq | icarus/db/emblrelease.it icarus/db/genbanknew.it icarus/db/genbankrelease.it icarus/db/genecards.it icarus/db/interpro.it icarus/db/medlinenew.it icarus/db/refseqnew.it icarus/db/refseqpnew.it | Added a getReleaseCommand, so prisma can set the release number after an update |
| 2007/08/01 | kegg | icarus/db/lcompound.i icarus/db/lcompound.is | Added a new Chebi ID field |
| 2007/08/01 | domo | icarus/db/domo.it | Change so prisma will download domo from the ebi, as the original download site no longer exists. Note that the domo data is static |
| 2007/08/01 | embl | icarus/db/emblnew.it icarus/db/emblnewfiles.it | Change to include the expanded and annotated contig files in the embl updates. |
| 2007/08/01 | system | icarus/db/dbxref.i | Change which allows to make hypertext links to uniprot from EMBL/GenBank feature tables |
| 2007/08/01 | embl | icarus/db/embl.is | Fix for a problem with constructing contig sequences when tincaching is enabled |
| 2007/08/01 | kegg | icarus/db/kegg_species.i | updated kegg species mapping file |
| 2007/07/31 | geneseq | icarus/db/geneseq.is | Correction for a problem with sequences during indexing |
| 2007/07/30 | pdb | icarus/db/pdb.it icarus/db/pdbmodel.it | Correction for the address of the USA download site |
| 2007/07/25 | medline | icarus/db/medlinecommon.i | Fix for a problem which caused EC numbers ending up in the CAS number index |
| 2007/07/24 | genbank embl refseq | icarus/db/gbemblcommon.is icarus/db/genbank.is icarus/db/genbankcommon.i | Added ECNumber and Molecular weight for refseqp and added handling of the PRIMARY line in refseq |
| 2007/07/24 | pdb | icarus/db/pdb.it icarus/db/pdbmodel.it | Changes to allow prisma to download the newly remdiated PDB datafiles. The changes have no effect in SRS but you may need to check that external software (like structure viewers) is compatable with the new data. See http://remediation.wwpdb.org/ for more information. Note that by default we download pdb from the ebi (European) site. If you wish to download from the US site, please edit the file, commenting out/in the relevant lines |
| 2007/07/23 | geneseq | icarus/db/geneseq.is | Change to provide more information in fasta headers with geneseq sequences |
| 2007/07/18 | uniprot ipi | icarus/db/swissprot.is | Change to allow for the use of a "n" in EC numbers (expected to appear in in uniprot in the near future) |
| 2007/07/17 | system | icarus/db/dbxref.i icarus/db/href.i | Added support for the new phargkb link in uniprot. Note that the new dbxref.i and href.i files need to be merged with your copies of these files in SRSSITE |
| 2007/06/29 | chebi | icarus/db/chebi.i icarus/db/chebi_schema.i icarus/db/chebidatamodel.i | schema update for release chebi 34 and fixes for several display problems |
| 2007/06/28 | system | icarus/db/mesh.it | Change to make sure we only download the desc.xml file for the mesh database (mesh is used as a hidden database to provide synonyms) |
| 2007/06/28 | iprmatches | icarus/db/iprmatches.i icarus/db/iprmatches.it icarus/db/iprmatchestable.il srstags/srstags/web/views/iprmatchesentry/iprmatchesentry.jsp srstags/srstags/web/views/iprmatchesentry/iprmatcheslist.jsp | Changes to handle the new format of the iprmatches data, found in the match_complete.xml file which comes with release 15.1 of interpro. The changes are incompatible with the old match.xml file which came with earlier releases, you have to make sure you have the new datafile in place when you apply this fix, and re-index iprmatches |
| 2007/06/25 | system | icarus/db/standard.is | Minor fix so iword1a production will index the character 0. |
| 2007/06/22 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensemblgene.i icarus/db/ensembltranscript.i | Correction for the links from ensembl to entrezgene |
| 2007/06/21 | embl | icarus/db/embl.is | Change to allow for multiple genome projects, as is allowed in EMBL 91 |
| 2007/06/20 | srscheck | icarus/workflows/linkPhase.i | Fix for a problem where in some cases prisma would not build link indices for a newly indexed database |
| 2007/06/20 | embl | icarus/db/emblnew.it icarus/db/emblnewfiles.it | Fix for a problem where prisma would not remove obsolete files for the emblnew database |
| 2007/06/18 | system | icarus/db/dbxref.i icarus/db/href.i | Added a few new hypertext links for uniprot. Note that dbxref.i and href.i need to be merged with your copies of these files in SRSSITE |
| 2007/06/18 | genecards | icarus/db/genecards.is | Fix for wrong hypertext link to ensembl |
| 2007/06/14 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcore_schema.i | Small changes for ensembl release 45 |
| 2007/06/13 | kegg | icarus/db/lcommon.is | Fix for a harmless parsing error thrown when build readlinks from lenzyme |
| 2007/06/08 | uniprot ipi | icarus/db/swissprot.is | Added hypertext links for the Web Resources in the comment field |
| 2007/05/30 | genecards | icarus/db/genecards.is | Change to allow for the new BIOMOL line in genecards |
| 2007/05/30 | kegg | icarus/db/kegg_species.i | Latest version of kegg species mapping file |
| 2007/05/30 | omim | icarus/db/omim.is | improved (but not perfected) indexing of journal names in omim. Note that due to the nature of the text it is not possible to do it correct for all entries |
| 2007/05/29 | uniprot ipi | icarus/db/swisscommon.i icarus/db/swissprot.is | After 29 May 2007, uniprot will contain a new evidence field. We have added support for this new field, and also added the EC Number (from the description line) as a separate field |
| 2007/05/29 | genecards | icarus/db/genecardstar.it | Fix for a reformatcommand which might fail on linux systems |
| 2007/05/25 | reactome | icarus/db/reactome.i icarus/db/reactome_schema.i | Change for some schema changes in version 21 of reactome. Note that these files expect the database name to be Reactome21 |
| 2007/05/25 | genecards | icarus/db/genecards.i | Corrected a wrong defintions for the link to goterm |
| 2007/05/25 | kegg system | icarus/db/kegggenes.i icarus/db/kegggenes_na.it icarus/db/kegggenome.it icarus/db/keggorthology.i icarus/db/keggorthology.it icarus/db/ren_kegggenes.pl icarus/db/srsdb.i | The recent change of the kegg download site, with the data for the kegg genes databases located in species specific subdirectories has resulted in very poor update performance by prisma (due to the large number of directories to check, and the poor connectivity to the kegg download site). So we have changed the download strategy to downloads the kegg genes tarball instead. Since this also provides the data for the kegg genome and kegg orthology databases, we also no longer do separate downloads for those. Note that we now no longer have the kegggenesdata and keggorthologydata helper libraries, and we expect the data for the kegggenome and keggorthology databases in the same directory as the kegggenes databases (see the changes is srsdb.i). The actual download process for the tarball is linked to the kegggenome database, so you must enable this library if you want prisma to update the kegggenes databases. Note that this update also requires you to update SRSLION/prisma/pretransPhase.i, otherwise prisma will get the dependies wrong. If you use prisma to udpate your icarus files, or the updateconfig script, please disable the kegggenesdata and keggorthologydata libraries before you do that. |
| 2007/05/10 | entrezgene | icarus/db/entrezgene.is | Change to the entrezgene parser so GO identifiers are indexed in the format GO:1234567 |
| 2007/05/10 | dbest | icarus/db/dbest.i icarus/db/dbest.is srstags/srstags/web/views/dbestentry/dbest.jsp | Modification to allow for the display of map submitter information |
| 2007/05/03 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcore_schema.i | Updates for ensembl release 44. There are some minor schema changes, which do not affect data retrieval/display |
| 2007/04/25 | system | icarus/db/standard.is | Fix for entry names containing things like XXXX_0_XXXX in gcg format files to prevent parsing entering the wrong section of a production |
| 2007/04/20 | transfac | icarus/db/transfaccommon.is | Fixed the binding site parsing so display fnuctions properly |
| 2007/04/16 | embl | icarus/db/embl.is | removed a duplicate genomeProject production |
| 2007/04/12 | geneticcode | icarus/db/geneticcode.i | Removed sorting from name index. Multiple values present due to database updates |
| 2007/04/12 | kegg | icarus/db/kegg_images.i icarus/db/kegg_species.i icarus/db/kegggenes_na.it icarus/db/kegggenome.it icarus/db/keggorthology.it icarus/db/lcompound.i icarus/db/lcompound.is icarus/db/lcompound.it icarus/db/ldrug.it icarus/db/lenzyme.is icarus/db/lenzyme.it icarus/db/lglycan.is icarus/db/lglycan.it icarus/db/lreaction.is icarus/db/lreaction.it icarus/db/pathwaytar.it srstags/srstags/web/views/lcompoundentry/lcompgeneral.jsp | The people at Pathway Inc. have reorganised their download area (it now more resembles the academic site). We have changed the .it files for the various kegg databases so we will donwload the correct data. Also a few other changes for fieldnames in lglycan and lreaction, and we allow for the new sequence field in lcompound |
| 2007/04/05 | system | icarus/db/dbxref.i icarus/db/href.i | Change to allwo for the new hypertext link to burulist in uniprot. Note that dbxref.i and href.i need to be merged with your copies of these file in SRSSITE |
| 2007/04/03 | system uniprot ipi | icarus/db/dbxref.i icarus/db/href.i icarus/db/swissprot.is | Change in the way we do hypertext links from uniprot to ensembl, ensuring we correctly go either to ensembl data locally in SRS or to the ensembl website. Please merge the new versions of dbxref.i and href.i with your copies of these files in SRSSITE |
| 2007/04/03 | entrezgene | icarus/db/entrezgene.i icarus/db/entrezgene_dm.i | Change to make sure protein names are displayed in the entrezgene entry |
| 2007/04/03 | go_xml system | icarus/db/go.is icarus/db/href.i | Correction for hypertext links to evidence identifiers in RGD (RatGenomeDatabase). please merge the new href.i file with your copy of that file in SRSSITE |
| 2007/04/03 | genecards | icarus/db/genecards.i | Updated the link definition for genecars to uniprot to use the uniprot primary accession number. After applying this update, please rebuild the genecards/uniprot link indices ("srsbuild i genecards uniprot_swissprot; srsbuild -i uniprot_trembl") |
| 2007/03/28 | system | icarus/db/href.i | Correction for hypertext links to ensembl. Please merge the new version of href.i with your copy of that file in SRSSITE |
| 2007/03/28 | genbank embl refseq | icarus/db/gbemblcommon.is | Small change so we no longer loose the end of line character in the display of translations of sequence features |
| 2007/03/26 | kegg | icarus/db/kegggenes.is | Fix for a problem with displaying html-ized GIDs in tables |
| 2007/03/21 | system uniprot ipi | icarus/db/href.i icarus/db/swissprot.is | Correcttion for the external hypertext link to merops. Note that the changes in href.i need to be merged with your copy of that file in SRSSITE |
| 2007/03/21 | medline | srstags/srstags/web/views/medlineentry/medlineentry.jsp srstags/srstags/web/views/medlineentry/medlineresults.jsp | Following customer feedback we have added hypertext links to PubMed at the ncbi to our display of medline data. |
| 2007/03/21 | srscheck | icarus/workflows/getSystemLibs.i | Small change in logic to make sure srs does not try to build sort sets for virtual RDB libraries |
| 2007/03/20 | kegg | icarus/db/kegg_species.i | Updates species mapping file for the kegg databases |
| 2007/03/19 | dbest | icarus/db/dbest.is | Change to allow for lower case sequence characters |
| 2007/03/19 | embl genbank refseq | icarus/db/embl.is icarus/db/emblcommon.i icarus/db/gbemblcommon.i icarus/db/genbank.is icarus/db/genbankcommon.i | Changes to allow for the GenomeProject field in embl, which will appear in the next release 90, soon available. We made this a searchable field, and also made it searchable for genbank (we were already displaying it for genbank. Note that after applying this update, alltext searches in embl/genbank/refseq will fail due to missing GenomeProject indices. Once the GenomeProject field for all databases in embl or genbank format has been indexed this will work again. You may want to schedule downtime or use an alternative SRS installation to build the GenomeProject indices. You can also edit emblcommon.i and genbankcommon.i to keep the GenomeProject field a non-indexed field. There is a comment in these files indicationg which line needs commenting out for that. |
| 2007/03/09 | reactome | icarus/db/reactome.i icarus/db/reactome_schema.i | Minor changes for reactome20. Note that reactome.i expects the database to be called "Reactome20" |
| 2007/03/07 | kegg | icarus/db/kegggenes.is | Change needed as the Kegg folks have renamed the "ORTHOLOG" field tag to "ORTHOLOGY" for the kegggenes dataset |
| 2007/03/07 | system | icarus/db/dbxref.i icarus/db/href.i | Change to allow for the new CYGD reference in the latest release of uniprot |
| 2007/03/07 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcommon.i icarus/db/ensemblcore_schema.i icarus/db/exondatamodel.i | Changes for ensembl release 43 and added missing link definitions for the ensemble gene databases |
| 2007/03/07 | kegg | icarus/db/lreaction.i | Reversed addition of Remark field definition in this file - already defined in srsgen.i |
| 2007/03/06 | dbest dbgss | icarus/db/dbest.it icarus/db/dbgss.it | Change so we use the .gz files for downloads of dbest and dbgss instead of the .Z files |
| 2007/02/22 | system | icarus/db/dbxref.i icarus/db/href.i | Added support for the new Cornea-2DPAGE, DOSAC-COBS-2DPAGE and REPRODUCTION-2DPAGE in uniprot. Note that the new href.i and dbxref.i files need to be merged with your copies of that file in SRSSITE |
| 2007/02/21 | userdna userprotein | icarus/db/userdna.i icarus/db/userprotein.i | Increased maxline to 500 to allow for longer header lines |
| 2007/02/20 | kegg | icarus/db/lreaction.i icarus/db/lreaction.is srstags/srstags/web/views/lreactionentry/lreactgeneral.jsp | Added Remark section for Reactions |
| 2007/02/20 | ensembl_mysql emboss | icarus/db/ExonsandIntrons.il icarus/db/OutputExons.il icarus/db/OutputPeptides.il icarus/db/OutputTranscripts.il icarus/db/UTRandCDS.il icarus/db/ensemblRDB.i icarus/db/ensemblaffy.i icarus/db/ensemblcommon.i icarus/db/ensemblgene.i icarus/db/ensemblmarker.i icarus/db/ensemblseq.i icarus/db/ensembltranscript.i icarus/lion/packages/emboss.ip icarus/lion/packages/ensemblRDB.ip srstags/srstags/web/views/ensemblmarker/marker.jsp | Various fixes/improvements for ensembl: Corrected some link definitions, added links to Genbank/DDBJ, added Zebrafish markers, added Affy data for Zebrafish, C.elegans, Chimp and Mosquito. Fixed problems with command line fasta sequence retrieval with transcripts. Some restructuring to make adding new datasets easier |
| 2007/02/19 | srscheck | icarus/workflows/srsCheckMain.i | Removed icaIsDebug parameter - no longer useable |
| 2007/02/16 | srscheck | icarus/workflows/coreCheckClasses.i | Fix for a problem when using the -user mode of srscheck, resulting in indexfilenames fused to the directory name |
| 2007/02/13 | pdb | icarus/db/pdb.i | Change so we no longer see the Broken Pipe error message when indexing pdb |
| 2007/02/09 | uniseq | icarus/db/uniseq.is | Change to correct for a format change which caused the start/end/utr fields to be empty, and fix for a data display issue with the last sequence in a block of ests in the data file |
| 2007/02/07 | uniest | icarus/db/uniest.is | Change to allow for refseq style Accession numbers |
| 2007/02/05 | kegg | icarus/db/ldrug.i icarus/db/ldrug.is srstags/srstags/web/views/ldrugentry/ldrugentry.jsp | Changes to allow for the new Activity field in the kegg drug database |
| 2007/02/02 | uniest unigene uniseq | icarus/db/uniest.i icarus/db/uniest.is icarus/db/unigene.it icarus/db/uniseq.i icarus/db/uniseq.it srstags/srstags/web/views/uniestentry/uniestentry.jsp | Changes needed to handle uniest entries with tens of thousends of est sequences and the fact that uniseq now has so many entries that the ID structure we use is no longer sufficient. Also a fix so prisma does not download a number of files from the unigene ftp site which result in duplicate entries. Note that after this update you must re-index both unigene and uniest and all links to/from these databases |
| 2007/01/29 | kegg | icarus/db/pathwaytar.it | Change to the command which removes obsolete pathway files so it does not result in a failure if there are no obsolete files |
| 2007/01/29 | kegg | icarus/db/kegg_species.i | updated kegg species mapping file |
| 2007/01/25 | system | icarus/db/mesh.it | Change so prisma will download the 2007 files for mesh |
| 2007/01/25 | kegg | icarus/db/kegggenes.is icarus/db/kegggenes_aa.i icarus/db/kegggenes_na.i | Changed kegggenes to use only index-links, as on some systems it has become difficults to build read-links |
| 2007/01/25 | reactome | icarus/db/reactome.i icarus/db/reactome_schema.i | Changes for release 19 of reactome. Note that we expect the database name to be Reactome19. You can modify this by editing reactome.i |
| 2007/01/25 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcore_schema.i | Schema and database name changes for ensembl 42 (MySql) |
| 2007/01/25 | kegg | icarus/db/kegg_species.i | latest species mapping file for the kegg databases |
| 2007/01/17 | genecards | icarus/db/genecards.is | Another fix to extend array to 50 elements |
| 2007/01/15 | ensembl_mysql | icarus/db/ensemblRDB.i | Added change for OMIM identifier for linking |
| 2007/01/15 | system | icarus/db/loader.i | Changed Interpro field used in Description View to use DF_Name |
| 2007/01/10 | system uniprot ipi | icarus/db/dbxref.i icarus/db/swissprot.is | Change to allow for dip and maizegdb ij the DR lines of uniprot. Please note that dbxref.i needs to be installed in SRSSITE |
| 2007/01/04 | srscheck | icarus/workflows/moveIndicesPhase.i | fix for srscheck/srsdo/srscheck reporting that virtual libs need rebuilding |
| 2006/12/22 | genecards | icarus/db/genecards.is | Minor fix for araay element out of bounds problem |
| 2006/12/21 | system | icarus/db/href.i | Added href for DIP and changed HREF for Gene3D |
| 2006/12/21 | uniprot ipi | icarus/db/swissprot.is | Added link production for DIP, changed link production for Gene3D |
| 2006/12/21 | go_xml | icarus/db/go.is | Increased the limit on number of associations displayed,and fixed a layout problem with associations |
| 2006/12/21 | genecards | icarus/db/genecards.is | Some fixes to prevent parsing errors in the bioalma section |
| 2006/12/19 | go_xml | icarus/db/go.i icarus/db/go.is | Changes needed for the disappeaance of the "Number of associtaions" field, which caused no associations to be displayed at all |
| 2006/12/18 | system | icarus/db/srsgen.i | Extended id range for Sequence_Id to cope with > 1000 subentries within UNIGENE/UNIEST databases |
| 2006/12/15 | kegg | icarus/db/lcommon.is | Added OMIM to list of db xrefs |
| 2006/12/15 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensemblgene.i icarus/db/ensemblgenemodel.i icarus/db/ensembltranscript.i | Fixes/corrections of orthologs in the ensembl gene display, and corrections for link annotations which might cause ensembl to be queried when it should not |
| 2006/12/13 | genecards | icarus/db/genecardstar.it | Correction for a postprocessing command used for the genecards tar ball, which in some shells could result in the deletion of the tarball |
| 2006/12/13 | entrezgene | icarus/db/entrezgene.is | Fix for incorrect processing of some Interactions information |
| 2006/12/12 | genecards system | icarus/db/genecards.i icarus/db/genecards.is icarus/db/genecardstar.it icarus/db/href.i srstags/srstags/web/views/genecardsentry/genecardsentry.jsp | Changes to handle genecards version 2.35. The Genecards distribution file has changed, so please read the remarks at the top of genecards.i on how to install genecards |
| 2006/12/12 | entrezgene | icarus/db/entrezgene.is | Fix for incorrect processing of some Interactions information |
| 2006/12/05 | uniprot ipi | icarus/db/swissprot.is | Fix for GENE3d link in IPI which is different to the in UNIPROT |
| 2006/12/04 | uniprot ipi | icarus/db/swissprot.is | Updated regularexpression for new version of Gene3D cross references |
| 2006/11/27 | pdb | icarus/db/pdb.it | Small change in the way we try to read the file listings fpr pdb at the rcsb frp site. This should prevent prisma from hanging in the check state fpr pdb |
| 2006/11/24 | hmmer pfam | icarus/db/hmmpfam.it icarus/db/pfama.it icarus/db/pfamb.it icarus/db/pfamc.it icarus/db/pfamhmm.it icarus/db/pfamseed.it icarus/db/swisspfam.it | Change to allow for the change of the pfam data downloads site from ftp.genetics.wustl.edu to selab.janelia.org |
| 2006/11/20 | system | icarus/db/dbxref.i icarus/db/href.i | Changes to allow for Drugbank, HPA and euHCVdb in the uniprot cross references section |
| 2006/11/15 | uniref | icarus/db/uniref.is icarus/db/unirefcommon.i srstags/srstags/web/views/unirefentry/uniref.jsp | Added support for the uniparc ID in uniref |
| 2006/11/14 | uniprot ipi | icarus/db/swissprot.is | Change to allow for a change in the format of the ID line in uniprot entries. |
| 2006/11/14 | uniref | icarus/db/uniref.is icarus/db/unirefcommon.i | Change to allow for the new isSeed parameter in uniref members |
| 2006/11/10 | kegg | icarus/db/lenzyme.is | Change to allow for the renaming of the OTHER_REAC tag to ALL_REAC. We keep calling this the OtherReaction field |
| 2006/11/08 | emboss | icarus/lion/emboss/dreg.i icarus/lion/emboss/fuzzpro.i | Corrections for some errors in the application definitions for dreg and fuzzpro |
| 2006/11/06 | medline | icarus/db/medline.is | Added code to eliminate various very common words from the medline generic text indices - this behaviour can by modified by editing the stopwords list at the top of medline.is |
| 2006/11/06 | geneseq | icarus/db/aageneseq.i icarus/db/geneseq.is | Improved display of patent assignee field |
| 2006/11/03 | kegg | icarus/db/lreaction.i icarus/db/lreaction.is srstags/srstags/web/views/lreactionentry/lreactgeneral.jsp | Changes to allow for the new GLYCAN and COMPOUND lines in lreaction |
| 2006/11/03 | kegg | icarus/db/kegg_species.i | latest update for the kegg species mapping file |
| 2006/10/31 | medline | icarus/db/medline.i | Added comments about the different databases which make up medline in SRS |
| 2006/10/31 | blast | icarus/db/blast.is | Some changes for more reliable hypertext links to SRS entries for blast hits |
| 2006/10/26 | kegg | icarus/db/pathwaytar.it | Change so we no longer unpack all 500000 files in the pathway distribution tarball, but only the html and gif files we need (about 80000). Also added code to remove obsolete files |
| 2006/10/26 | kegg | icarus/db/pathway.is | Fixed some parsing errors for map/omim entries, and enabled hypertext links to the kegg genes databases |
| 2006/10/25 | entrezgene | icarus/db/entrezgene.is | small change to fix a problem with pebmed hypertext links in the generif section |
| 2006/10/23 | geneseq | icarus/db/aageneseq.i | Changed the ID type used for priority subentries, as the one we used proviously was causing problems due to overlapping subentry reanges. Please note that after applying this change you will have to re-index nageneseq and aageneseq, and that users may encounter errors until that has been done |
| 2006/10/18 | ensembl_mysql | icarus/db/ensemblRDB.i | Changes for ensembl release 41. Note that only the names of the mysql databases have changed, and that these changes also can be picked up from mysql if you have the most recent version of rdbaccess.i |
| 2006/10/13 | reactome | icarus/db/reactome.i icarus/db/reactome.is icarus/db/reactome.it icarus/db/reactome_datamodel.i icarus/db/reactome_schema.i | Some additional changes needed to handle some entries in reactome 18 |
| 2006/10/12 | system | icarus/db/mesh.it | Change to make sure that prisma downloads the 2006 version of mesh |
| 2006/10/12 | emboss | icarus/lion/emboss/afEmboss.is icarus/lion/emboss/antigenic.i icarus/lion/emboss/antigenic.it icarus/lion/emboss/backtranseq.i icarus/lion/emboss/backtranseq.it icarus/lion/emboss/biosedn.i icarus/lion/emboss/biosedn.it icarus/lion/emboss/biosedp.i icarus/lion/emboss/biosedp.it icarus/lion/emboss/btwisted.i icarus/lion/emboss/btwisted.it icarus/lion/emboss/cai.i icarus/lion/emboss/cai.it icarus/lion/emboss/chaos.i icarus/lion/emboss/chaos.it icarus/lion/emboss/charge.i icarus/lion/emboss/charge.it icarus/lion/emboss/checktrans.i icarus/lion/emboss/checktrans.it icarus/lion/emboss/chips.i icarus/lion/emboss/chips.it icarus/lion/emboss/compseqn.i icarus/lion/emboss/compseqn.it icarus/lion/emboss/compseqp.i icarus/lion/emboss/compseqp.it icarus/lion/emboss/consn.i icarus/lion/emboss/consn.it icarus/lion/emboss/consp.i icarus/lion/emboss/consp.it icarus/lion/emboss/cpgplot.i icarus/lion/emboss/cpgplot.it icarus/lion/emboss/cpgreport.i icarus/lion/emboss/cpgreport.it icarus/lion/emboss/cusp.i icarus/lion/emboss/cusp.it icarus/lion/emboss/cutseqn.i icarus/lion/emboss/cutseqn.it icarus/lion/emboss/cutseqp.i icarus/lion/emboss/cutseqp.it icarus/lion/emboss/dan.i icarus/lion/emboss/dan.it icarus/lion/emboss/degapseqn.i icarus/lion/emboss/degapseqn.it icarus/lion/emboss/degapseqp.i icarus/lion/emboss/degapseqp.it icarus/lion/emboss/descseqn.i icarus/lion/emboss/descseqn.it icarus/lion/emboss/descseqp.i icarus/lion/emboss/descseqp.it icarus/lion/emboss/diffseqn.i icarus/lion/emboss/diffseqn.it icarus/lion/emboss/diffseqp.i icarus/lion/emboss/digest.i icarus/lion/emboss/digest.it icarus/lion/emboss/distmatn.i icarus/lion/emboss/distmatp.i icarus/lion/emboss/dotmatchern.i icarus/lion/emboss/dotmatchern.it icarus/lion/emboss/dotmatcherp.i icarus/lion/emboss/dotmatcherp.it icarus/lion/emboss/dotpathn.i icarus/lion/emboss/dotpathn.it icarus/lion/emboss/dotpathp.i icarus/lion/emboss/dotpathp.it icarus/lion/emboss/dottupn.i icarus/lion/emboss/dottupn.it icarus/lion/emboss/dottupp.i icarus/lion/emboss/dottupp.it icarus/lion/emboss/dreg.i icarus/lion/emboss/dreg.it icarus/lion/emboss/einverted.i icarus/lion/emboss/einverted.it icarus/lion/emboss/embossViews.i icarus/lion/emboss/eprimer3.i icarus/lion/emboss/eprimer3.it icarus/lion/emboss/eprimers.i icarus/lion/emboss/eprimers.it icarus/lion/emboss/equicktandem.i icarus/lion/emboss/equicktandem.it icarus/lion/emboss/est2genome.i icarus/lion/emboss/est2genome.it icarus/lion/emboss/etandem.i icarus/lion/emboss/etandem.it icarus/lion/emboss/extractseqn.i icarus/lion/emboss/extractseqp.i icarus/lion/emboss/freakn.i icarus/lion/emboss/freakn.it icarus/lion/emboss/freakp.i icarus/lion/emboss/freakp.it icarus/lion/emboss/fuzznuc.i icarus/lion/emboss/fuzzpro.i icarus/lion/emboss/fuzztran.i icarus/lion/emboss/garnier.i icarus/lion/emboss/garnier.it icarus/lion/emboss/geecee.i icarus/lion/emboss/getorf.i icarus/lion/emboss/getorf.it icarus/lion/emboss/helixturnhelix.i icarus/lion/emboss/helixturnhelix.it icarus/lion/emboss/hmoment.i icarus/lion/emboss/hmoment.it icarus/lion/emboss/iep.i icarus/lion/emboss/iep.it icarus/lion/emboss/infoalignn.i icarus/lion/emboss/infoalignn.it icarus/lion/emboss/infoalignp.i icarus/lion/emboss/infoalignp.it icarus/lion/emboss/infoseqn.i icarus/lion/emboss/infoseqn.it icarus/lion/emboss/infoseqp.i icarus/lion/emboss/infoseqp.it icarus/lion/emboss/isochore.i icarus/lion/emboss/isochore.it icarus/lion/emboss/marscan.i icarus/lion/emboss/maskseqn.i icarus/lion/emboss/maskseqn.it icarus/lion/emboss/maskseqp.i icarus/lion/emboss/maskseqp.it icarus/lion/emboss/matchern.i icarus/lion/emboss/matchern.it icarus/lion/emboss/matcherp.i icarus/lion/emboss/matcherp.it icarus/lion/emboss/megamerger.i icarus/lion/emboss/megamerger.it icarus/lion/emboss/merger.i icarus/lion/emboss/merger.it icarus/lion/emboss/msbarn.i icarus/lion/emboss/msbarn.it icarus/lion/emboss/msbarp.i icarus/lion/emboss/msbarp.it icarus/lion/emboss/needlen.i icarus/lion/emboss/needlen.it icarus/lion/emboss/needlep.i icarus/lion/emboss/needlep.it icarus/lion/emboss/newcpgreport.i icarus/lion/emboss/newcpgreport.it icarus/lion/emboss/newcpgseek.i icarus/lion/emboss/newcpgseek.it icarus/lion/emboss/octanol.i icarus/lion/emboss/octanol.it icarus/lion/emboss/palindrome.i icarus/lion/emboss/palindrome.it icarus/lion/emboss/pasteseqn.i icarus/lion/emboss/pasteseqp.i icarus/lion/emboss/patmatdb.i icarus/lion/emboss/patmatdb.it icarus/lion/emboss/patmatmotifs.i icarus/lion/emboss/patmatmotifs.it icarus/lion/emboss/pepcoil.i icarus/lion/emboss/pepcoil.it icarus/lion/emboss/pepinfo.i icarus/lion/emboss/pepinfo.is icarus/lion/emboss/pepinfo.i |