Difference between revisions of "BLAST/BLAT Page"
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Revision as of 15:32, 10 December 2007
The Wormbase BLAST/BLAT page can be accessed by the "Blast / Blat" link on the top navigation bar.
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.