Programs

swp
swp is a fast peptide sequence search that utilizes the S-W (Smith-Waterman) algorithm. swp reads in one or more FASTA queries from a file, performs a linear local S-W search for each query, and generates one separate BLAST report for each query.

To be used to check for the presence in the database of protein sequences related to a protein query sequence

swx
swx is a fast nucleotide sequence search that utilizes the S-W (Smith-Waterman) algorithm. swx reads in one or more FASTA queries from a file, performs a linear local S-W frame-shift search for each query, and generates one separate BLAST report for each query.

To be used to check for the presence of a possible protein sequence encoded in an unknown or low-quality DNA query sequence.

tswn (not available)
tswn is a fast peptide sequence search that utilizes the S-W (Smith-Waterman) algorithm. tswn reads in one or more FASTA queries from a file, performs a linear local S-W frame-shift search for each query, and generates one separate BLAST report for each query.

To be used to check for the presence of a DNA sequence or clone matching with a protein query sequence.

Parameters

M=Matrix
Specify an alternate scoring matrix for SWP, SWX, and TSWN. The default matrix is BLOSUM62 (Henikoff & Henikoff, 1992). The valid alternative choices include: other BLOSUMs, PAM120, PAM250, DAYHOFF, GONNETand IDENTITY.

S=Score threshold
Cutoff score for reporting high-scoring segment pairs (HSP). The default value is set to 100.
HSPs are reported for a database sequence only if the statistical significance ascribed to them is at least as high as would be ascribed to a lone HSP having a score equal to the S value. Higher S values are more stringent, leading to fewer chance matches being reported.

V=number of one-line summaries
Restricts the number of short descriptions of matching sequences reported to the number specified; default limit is set to 20 descriptions.

B=number of alignments
Restricts database sequences to the number specified for which high-scoring segment pairs (HSPs) are reported; the default limit is set to 20 alignments.

Protein databases

non redundant

The protein database is constructed from SwissProt, SwissProt updates, TrEMBL, TrEMBL updates, Genpept, Genpept updates, and a small subsection of PIR containing sequences not in the other databases (usually for good reasons).Updated weekly, usually on weekends.

SwissProt

The most recent full release of SwissProt. Does not include updates.

SwissProt/TrEMBL/TrEMBL_NEW

A combination of SwissProt and TrEMBL (including updates but not REM-TrEMBL). This database contains all consolidated proteins and ORFs (udated weekly).

yeast (S. cerevisiae)

The protein database contains all annotated yeast ORFs (updated occasionally).

trest **** WARNING!

This is a database of protein sequences derived from ESTs sequencing data (human, mouse, rat, drosophila). The ESTs are clustered, contigs are generated from the clusters by an unpublished procedure and translated.

It might contain useful sequences, but the user should be aware of the possible errors that are likely to be found in this database.

trgen **** WARNING!

This is a database of protein sequences derived from human genomic sequencing data. The genomic sequence are analysed by the program GenScan and the putative coding sequences in exons are translated.

It might contain useful sequences, but the user should be aware of the possible errors that are likely to be found in this database.

RefSeq

Reference protein sequences from NCBI (updated weekly).

Bacteria

All the bacterial and microbial proteomes (updated weekly).