Introduction to the BLAST Tool


The BLAST Tool, which is provided as part of the Genes and proteins Quick Search option accessed under the 'View more search options' link of the main search page, allows searches of the BKL by protein sequence using BLASTp (BLAST). The search returns a list of the protein(s) associated with the sequence entered, with hyperlinks to the corresponding Locus Reports.

Blast tool

BLAST tool

Use the BLAST Tool to:

Performing BLAST Searches

The BLAST form is a simple interface that uses blastp to compare an amino acid sequence against all proteins contained within the BKL for the species selected.

Please note: Nucleotide BLAST searches are not supported.

To perform a BLAST search:

  1. Paste the sequence into the sequence text area. Any non-letter characters are filtered out of the sequence automatically. To BLAST multiple sequences (up to five), paste the sequences into the sequence text area in FASTA format, making sure to maintain the ">" separator, which allows the algorithm to distinguish each sequence as separate, as below:

    > gi|28199993|gb|AAO31745.1| BRCA1 [Didelphis virginiana]

    > gi|28199991|gb|AAO31744.1| BRCA1 [Dendrolagus matschiei]

    > gi|28199989|gb|AAO31743.1| BRCA1 [Macropus robustus]

  2. Limit the search by setting the minimum percentages for identity and positives.

  3. Deselect the Filter query sequence feature if you wish to turn off the default SEG filter.

    The SEG filter masks out small regions of low complexity in the sequence. A low complexity region is a portion of the amino acid sequence of a protein that is composed of only a few of the 20 possible amino acids. Low complexity regions tend to have significant BLAST similarities to many unrelated proteins, often obscuring real similarities that may be present.

  4. Click blast to run the query.

  5. The search results appear as a list of BLAST scores. Details about BLAST analyses are provided here.

Viewing Results

Results of BLAST Searches are listed with gene symbol, species, GenBank accession number, synonyms and title line, the match length, percent identity, percent similarity, score, and E-value.

Viewing BLAST Results

Viewing BLAST Results

Results are hyperlinked to the corresponding BKL Locus Reports and GenBank reports.

When running a multi-sequence BLAST, tabs at the top of the BLAST results page separate results by each sequence input into the BLAST search, with the number of BLAST hits listed in parentheses.

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