BLAST/BLAT Page

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.