Difference between revisions of "BLAST/BLAT Page"
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| − | The Wormbase BLAST/BLAT page can be accessed by the "Blast / Blat" link on the top navigation bar. | + | The Wormbase BLAST/BLAT page can be accessed by the "Blast / Blat" link on the top navigation bar. |
| − | The components of the page: | + | <span style="color: rgb(255, 0, 0);">'''NOTE: THIS PAGE IS OUT OF DATE AND IN NEED OF UPDATE.'''</span> |
| + | |||
| + | <span style="color: rgb(255, 0, 0);">'''In particular, we have added additional databases for every species, and changed the way they are created (through the new update pipeline).'''</span> | ||
| + | |||
| + | |||
| + | |||
| + | The components of the page: | ||
$WORMBASE/cgi-perl/searches/blast_blat (CGI script) | $WORMBASE/cgi-perl/searches/blast_blat (CGI script) | ||
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'''Javascript''': display_results.js, search_form.js | '''Javascript''': display_results.js, search_form.js | ||
'''Temporary directory''': tmp/ | '''Temporary directory''': tmp/ | ||
| + | |||
| + | |||
| + | Supplementary scripts: | ||
| − | |||
| − | |||
$WORMBASE/util/admin/restart_blat.pl - Starts/checks BLAT servers | $WORMBASE/util/admin/restart_blat.pl - Starts/checks BLAT servers | ||
Run as a cron job: | Run as a cron job: | ||
0 4 * * * /usr/local/wormbase/util/admin/restart_blat.pl | mail -s "Status: restart_blat.pl" canaran@cshl.edu cron@tharris.org | 0 4 * * * /usr/local/wormbase/util/admin/restart_blat.pl | mail -s "Status: restart_blat.pl" canaran@cshl.edu cron@tharris.org | ||
| + | |||
$WORMBASE/update_scripts/dump_scripts/dump_nucleotide.pl - Dump nucl.fa for c_elegans blast database | $WORMBASE/update_scripts/dump_scripts/dump_nucleotide.pl - Dump nucl.fa for c_elegans blast database | ||
| − | The BLAST and BLAT databases for each release are located in: | + | |
| + | |||
| + | The BLAST and BLAT databases for each release are located in: | ||
| − | /usr/local/wormbase/databases/WS | + | /usr/local/wormbase/databases/WS<release_id>/ |
| + | |||
| − | |||
| − | WS | + | List of databases: |
| + | |||
| + | WS<release_id> | ||
|-- blast | |-- blast | ||
| |-- c_brenneri | | |-- c_brenneri | ||
| Line 97: | Line 109: | ||
|-- CHROMOSOME_*.dna | |-- CHROMOSOME_*.dna | ||
`-- CHROMOSOME_*.nib | `-- CHROMOSOME_*.nib | ||
| + | |||
| + | |||
| + | Notes: | ||
| − | + | *This list excludes supplementary and archival files. | |
| − | * This list excludes supplementary and archival files. | + | *c_elegans blast and blat databases are updated with each release. Others are stable and updated when needed. |
| − | * c_elegans blast and blat databases are updated with each release. Others are stable and updated when needed. | ||
Revision as of 17:01, 20 June 2008
The Wormbase BLAST/BLAT page can be accessed by the "Blast / Blat" link on the top navigation bar.
NOTE: THIS PAGE IS OUT OF DATE AND IN NEED OF UPDATE.
In particular, we have added additional databases for every species, and changed the way they are created (through the new update pipeline).
The components of the page:
$WORMBASE/cgi-perl/searches/blast_blat (CGI script) $WORMBASE/html/blast_blat/ Images: blank.png, minus.png, plus.png, sample_nucleotide.png, sample_peptide.png Template Toolkit templates: display_results.html, message_page.html, search_form.html CSS: blast_pages.css Javascript: display_results.js, search_form.js Temporary directory: tmp/
Supplementary scripts:
$WORMBASE/util/admin/restart_blat.pl - Starts/checks BLAT servers Run as a cron job: 0 4 * * * /usr/local/wormbase/util/admin/restart_blat.pl | mail -s "Status: restart_blat.pl" canaran@cshl.edu cron@tharris.org
$WORMBASE/update_scripts/dump_scripts/dump_nucleotide.pl - Dump nucl.fa for c_elegans blast database
The BLAST and BLAT databases for each release are located in:
/usr/local/wormbase/databases/WS<release_id>/
List of databases:
WS<release_id>
|-- blast
| |-- c_brenneri
| | `-- 2007_01_draft_assembly
| | |-- supercontigs.fa
| | |-- supercontigs.fa.nhr
| | |-- supercontigs.fa.nin
| | `-- supercontigs.fa.nsq
| |-- c_briggsae
| | |-- cb25
| | | |-- briggsae.CB25.dna.fa
| | | |-- briggsae.CB25.dna.fa.nhr
| | | |-- briggsae.CB25.dna.fa.nin
| | | `-- briggsae.CB25.dna.fa.nsq
| | |-- cb3
| | | |-- briggsae_cb3.fa
| | | |-- briggsae_cb3.fa.nhr
| | | |-- briggsae_cb3.fa.nin
| | | `-- briggsae_cb3.fa.nsq
| | |-- peptide.fa
| | |-- peptide.fa.phr
| | |-- peptide.fa.pin
| | `-- peptide.fa.psq
| |-- c_brugia
| | `-- bma1
| | |-- bma1.assembly.fa
| | |-- bma1.assembly.fa.nhr
| | |-- bma1.assembly.fa.nin
| | |-- bma1.assembly.fa.nsq
| | |-- bma1.pep.fa
| | |-- bma1.pep.fa.phr
| | |-- bma1.pep.fa.pin
| | `-- bma1.pep.fa.psq
| |-- c_elegans
| | |-- est.fa
| | |-- est.fa.nhr
| | |-- est.fa.nin
| | |-- est.fa.nsq
| | |-- formatdb.log
| | |-- genomic.fa
| | |-- genomic.fa.nhr
| | |-- genomic.fa.nin
| | |-- genomic.fa.nsq
| | |-- nucl.fa
| | |-- nucl.fa.nhr
| | |-- nucl.fa.nin
| | |-- nucl.fa.nsq
| | |-- peptide.fa
| | |-- peptide.fa.phr
| | |-- peptide.fa.pin
| | `-- peptide.fa.psq
| `-- c_remanei
| `-- 2005_08_20_assembly
| |-- genomic.fa
| |-- genomic.fa.nhr
| |-- genomic.fa.nin
| |-- genomic.fa.nsq
| |-- peptide.fa
| |-- peptide.fa.phr
| |-- peptide.fa.pin
| `-- peptide.fa.psq
|-- blat
|-- c_briggsae
| |-- cb25
| | |-- briggsae.CB25.dna.fa-cb25.NA_*.fa
| | `-- briggsae.CB25.dna.fa-cb25.NA_*.fa.nib
| `-- cb3
| |-- briggsae_cb3.fa-chr*.fa
| `-- briggsae_cb3.fa-chr*.fa.nib
`-- c_elegans
|-- CHROMOSOME_*.dna
`-- CHROMOSOME_*.nib
Notes:
- This list excludes supplementary and archival files.
- c_elegans blast and blat databases are updated with each release. Others are stable and updated when needed.
