search protein databases using a protein query (2024)

♦Max target sequences non-default value
Select the maximum number of aligned sequences to display Help

Maximum number of aligned sequences to display (the actual number of alignments may be greater than this).

Automatically adjust parameters for short input sequences Help

Automatically adjust word size and other parameters to improve results for short queries.

♦Expect threshold non-default value Help

♦Word size non-default value Help

The length of the seed that initiates an alignment. more...

♦Max matches in a query range non-default value Help

Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query. The algorithm is based upon //www.ncbi.nlm.nih.gov/pubmed/10890403

♦Matrix non-default value Help

Assigns a score for aligning pairs of residues, and determines overall alignment score. more...

♦Match/Mismatch Scores non-default value Help

Reward and penalty for matching and mismatching bases. more...

♦Gap Costs non-default value Help

Cost to create and extend a gap in an alignment. more...

♦Compositional adjustments non-default value Help

Matrix adjustment method to compensate for amino acid composition of sequences. more...

♦Template length non-default value Help

Total number of bases in a seed that ignores some positions. more...

♦Template type non-default value Help

Specifies which bases are ignored in scanning the database. more...

PSSM ♦PSSM non-default value

PSSM is uploaded... Clear

Upload PSSM Optional

Help

Set the statistical significance threshold to include a sequence in the model used by PSI-BLAST to create the PSSM on the next iteration.

♦DELTA-BLAST Threshold non-default value Help

Set the statistical significance threshold to include a domain in the model used by DELTA-BLAST to create the PSSM

♦Pseudocount non-default value Help

Pseduocount parameter. If zero is specified, then the parameter is automatically determined through a minimum length description principle (PMID 19088134). A value of 30 is suggested in order to obtain the approximate behavior before the minimum length principle was implemented.