sigscan

sigscan

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sigscan scans a signature such as that generated by the EMBOSS application siggen against a protein sequence database and generates files of scored hits and corresponding alignments.

Here is a sample session with sigscan:

% sigscan

Mandatory qualifiers:

[-sigin] (infile)

Name of signature file (input).

-database (seqall)

Name of the SWISS-PROT sequence database to search.

-targetf (infile)

Name of validation (input).

-thresh (integer)

Minimum length (residues) of overlap required for two hits with the same code to count as the same hit.

-sub (matrixf)

This is the scoring matrix file used when comparing sequences.

-gapo (float)

The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAMAT matrix for nucleotide sequences.

-gape (float)

The gap extension penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. You can usually expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception occurs when one or both sequences are single reads with possible sequencing errors, in which case you should expect many single base gaps. You can obtain this result by setting the gap open penalty to zero (or a very low value) and using the gap extension penalty to control gap scoring.

-nterm (menu)

Select number.

-nhits (integer)

Number of hits to output.

[-hitsf] (outfile)

Name of signature hits file (output).

[-alignf] (outfile)

Name of signature alignments file (output).