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Blast Help
Database:
  • Plant UniProt
    Downloaded from UniProt taxonomic divisions.
  • Genes
    The M. grisea (MG) genes from the MGOS site, and the rice (OS) genes from TIGR
  • EST libraries
    The M. grisea ESTs and rice ESTs generated for the original MGOS project. See descriptions.
  • EST contigs
    The EST Contigs assembled from the above described ESTs using the PAVE program.
  • Genomes
    The M. grisea genome sequence from Broad and the rice genome sequence from TIGR that was sequenced by the IRGSP.

BLAST:
For a better understanding of BLAST you can refer to the BLAST Course which explains the basics of the BLAST algorithm.
The following descriptions are copied from http://www.ncbi.nlm.nih.gov/BLAST/

BLAST program:
  • 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.

BLAST Parameters:

  • Filter
    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.
  • 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.

Result 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.
    tabular : the columns are

    Column Field Name
    1
    Query ID
    2
    Subject ID
    3
    % Identity
    4
    Alignment Length
    5
    Mismatches
    6
    Gap Openings
    7
    Query Start
    8
    Query End
    9
    Subject Start
    10
    Subject End
    11
    E-Value
    12
    Bit Score