[an error occurred while processing this directive] [an error occurred while processing this directive] Blast Help

Blast Help


NCBI BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs (Altschul et al., 1990). For a better understanding of BLAST you can refer to the BLAST Course which explains the basics of the BLAST algorithm.

Some of the description of BLAST parameters listed below were obtained from http://www.ncbi.nlm.nih.gov/BLAST/

BLAST Program:
The NCBI BLAST family of programs includes:

  • blastp
    compares an amino acid query sequence against a protein sequence database
  • blastn
    compares a nucleotide query sequence against a nucleotide sequence database
  • blastx
    compares a nucleotide query sequence translated in all reading frames against a protein sequence database
  • tblastn
    compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames
  • tblastx
    compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. Please note that tblastx program cannot be used with the nr database on the BLAST Web page.

Database:

Blast Parameters:

  • Filter
    Mask off segments of the query sequence that have low compositional complexity, as determined by the SEG program of Wootton & Federhen (Computers and Chemistry, 1993) or, for BLASTN, by the DUST program of Tatusov and Lipman (in preparation). 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.
    Filtering is only applied to the query sequence (or its translation products), not to database sequences. Default filtering is DUST for BLASTN, SEG for other programs.
    It is not unusual for nothing at all to be masked by SEG, when applied to sequences in SWISS-PROT, so filtering should not be expected to always yield an effect. Furthermore, in some cases, sequences are masked in their entirety, indicating that the statistical significance of any matches reported against the unfiltered query sequence should be suspect.
  • Expectation
    The statistical significance threshold for reporting matches against database sequences; the default value is 10, such that 10 matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported. Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported. Fractional values are acceptable.
  • Matrix
    Specify an alternate scoring matrix for BLASTP, BLASTX, TBLASTN and TBLASTX. The default matrix is BLOSUM62 (Henikoff & Henikoff, 1992). The valid alternative choices include: PAM40, PAM120, PAM250 and IDENTITY. No alternate scoring matrices are available for BLASTN; specifying the MATRIX directive in BLASTN requests returns an error response.
  • Gapped Alignments
    Whether to allow gapped alignments; either ON or OFF.
  • Word Size
    The size of the initial word that must be matched between the database and the query sequence.
  • Nucleic Mismatch
    Penalty for a mismatch in the BLAST™ portion of run.
  • Nucleic Match
    Reward for a match in the BLAST™ portion of run.

Blast Format Options:

  • Descriptions
    Restricts the number of short descriptions of matching sequences reported to the number specified; default limit is 100 descriptions. See also EXPECT.
  • Alignments
    Restricts database sequences to the number specified for which high-scoring segment pairs (HSPs) are reported; the default limit is 100. If more database sequences than this happen to satisfy the statistical significance threshold for reporting (see EXPECT below), only the matches ascribed the greatest statistical significance are reported.

  • Alignments Views

    pairwise : Standard BLAST alignment in pairs of query sequence and database match.
    Query-anchored with identities : The databases alignments are anchored (shown in relation to) to the query sequence. Identities are displayed as dashes, with mismatches displayed as single letter nucleotide abbreviations.
    Query-anchored without identities : Identities are shown as single letter nucleotide abbreviations.
    Flat Query-anchored with identities : The 'flat' display shows inserts as deletions on the query.
    Identities are displayed as dashes, with mismatches displayed as single letter nucleotide abbreviations.
    Flat Query-anchored without identities : The 'flat' display shows inserts as deletions on the query. Identities are shown as single letter nucleotide abbreviations.

Blast Return Result Options:

  • To web browser
    Your job will run immediately and return results directly to your Web browser in HTML format. Accession numbers that appear in the query and target loci names and descriptions will be hyperlinked to allow easy access to additional sequence information.

  • By E-mail
    The results will be sent within the body of email message, to the email address you entered.


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