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.

NOTE: THIS PAGE IS OUT OF DATE AND IN NEED OF UPDATE.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.