Biotechnology and Bioinformatics (1+1)

BLAST Search Parameters

1. Histogram

Display a histogram of scores for each search; default is yes

2. Descriptions

Restricts the number of short descriptions of matching sequences reported to the number specified

3. Alignments

Restricts database sequences to the number specified for which high-scoring segment pairs (HSPs) are reported; the default limit is 50. If more database sequences than this happen to satisfy the statistical significance threshold for reporting (see EXPECT and CUTOFF below), only the matches ascribed the greatest statistical significance are reported.

4. Expect

The statistical significance threshold for reporting matches against database sequences; the default value is 10.

5. Cutoff

Cutoff score for reporting high–scoring segment pairs (HSP). The default value is calculated from the EXCEPT value HSPs are reported for a database sequence only if the statistical significance ascribed to them is at least as high as would be ascribed to a lone HSP having a score equal to the CUTOFF value. Higher CUTOFF values are more stringent, leading to fewer chance matches being reported. Typically, significance thresholds can be more intuitively managed using EXPECT.

6. Matrix

Specify an alternate scoring matrix for BLASTP, BLASTX, TBLASTN and TBLASTX. The default matrix is BLOSUM62.The valid alternative choices include : PAM40, PAM120, PAM250

7. Strand

Restrict a TBLASTN search to just the top or bottom strand of the database sequences; or restrict a BLASTN, BLASTX or TBLASTX search to just reading frames on the top or bottom strand of the query sequence.

8. Filter

Mask off segments of the query sequence that have low compositional complexity or segments consisting of short-periodicity internal repeats. Filtering can eliminate statistically significant but biologically uninteresting reports from the blast output (e.g., hits against common acidic, - basic – or proline-rich regions), leaving the more biologically interesting regions of the query sequence available for specific matching against database sequences.

Low complexity sequence found by a filter program is substituted using the letter “N” in nucleotide sequence and the letter “X” in protein sequences Users may turn off filtering by using the “Filter” option on the “Advanced options for the BLAST server” page.

9. NCBI-gi

Causes NCBI gi identifiers to be shown in the output, in addition to the accession and /or locus name.