BLAST Parameters

Sequence format

FASTA
A common sequence format offered by most sequence and alignment editors. A sequence consists of a header line followed by sequence bases. A header line consists of a 'greater than' (>) symbol followed by the sequence name. A FASTA file can contain multiple sequences. For example:
>RL228e1
AGAAGAAGAGGTAGTAATTAGATCTGACAATTTCACGGACAATGCTAAAACTATAATAGTACAGCTGAAAGAACCTGT
AGAAATTAATTGTACAAGACCCCACAACAATACAAGAAGAAGGATAAGTATAGGACCAGGGAGAGCATTTTATGCAAC
>RL228e2
AGAAATTAATTGTACAAGACCCCACAACAATACAAGAAGAAGGATAAGTATAGGACCAGGGAGAGCATTTTATGCAAC
AGAAGAAGAGGTAGTAATTAGATCTGACAATTTCACGGACAATGCTAAAACTATAATAGTACAGCTGAAAGAACCTGT
GAAGAAGAGGTAGTAATTAGATCTGACAATTTCACGGACAATGCTAAAACTATAATAGTACAGCTGAAAG

BLAST parameters

Expect
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.
Word size
The minimum length of the initial exact match before an extension of the alignment is initiated. A bigger word size will produce less but more specific hits than a smaller word size. A smaller word size will produce more but less specific hits than a bigger word size.
Max target sequences
Maximum number of descriptions and alignments to keep. The default value is 50.
Match/Mismatch scores
For BLASTN, the scores are reward for a nucleotide match and penalty for a nucleotide mismatch.
Matrix
Scoring matrix name. The default matrix is BLOSUM62.
Gap costs
Cost to open a new gap and cost to extend an existing gap.
Filter (Low-complexity)

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.

Mask for lookup table only
This option masks only for purposes of constructing the lookup table used by BLAST. The BLAST extensions are performed without masking.

Mask for lower case letters
Choose to use lower case filtering in query and subject sequence(s).
Alignment
Choose to perform ungapped alignment.
Alignment output format
Standard BLAST alignment in pairs of query sequence and database match. For nucleotide, the matches are marked by a pipe symbol ("|") in between query and database sequence. For protein, the identical matches are marked by letter code with "homologous" substitutions (determined by the scoring matrix used) marked by "+" symbol in a line between the query and the database sequence.
Pairwise: Database alignments are shown in relation to the query sequence in pairwise fashion.
Query-anchored with identities: Database alignments are anchored and shown in relation to the query sequence. Identities are displayed as dots (.), with mismatches displayed as single letter abbreviations.
Query-anchored without identities: Query-anchored, but 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 dots (.), with mismatches displayed as single letter abbreviations.
Flat Query-anchored without identities: Flat query-anchored, but identities are shown as single letter abbreviations.
XML Blast output: Output in XML format.
Tabular: Simple tabular output with different aligment information separated according to tab delimited fields with field headers displayed at the top.
Tabular with comment lines: Tabular, but with comments on field headers.
Query genetic code
Genetic code tobe used to translate query sequences.
Database genetic Code
Genetic code to use to translate database sequences.
Other parameters
Users can further set other parameters for their BLAST search.