| Program name | Source | Description |
|---|
| BLAST |
GCG |
Blast on local databases |
| FastA |
GCG |
FastA on local databases. |
| FastX |
GCG |
FastX on local databases. |
| Fetch |
GCG |
Get a sequence from a GCG database. |
| GCGtoBLAST |
GCG |
Combines GCG format sequences into a Blast searchable database. |
| lfasta |
FastA |
local similarity searches showing local alignments. |
| LookUp |
GCG |
Find a sequence data base entry by SRS. |
| NetBLAST |
GCG |
Blast search at NCBI. |
| NetFetch |
GCG |
Interface to NetEntrez to get sequences from NetBlast search. |
| patmatdb |
EMBOSS |
Matching a Prosite motif against a Protein Sequence Database. |
| prdf2 |
FastA |
Calculates the probability of a similarity score using an extreme value distribution. |
| printsextract |
EMBOSS |
Preprocesses the PRINTS database for use with the program PSCAN |
| ProfileScan |
GCG |
Finds motifs in a database of profiles. |
| ProfileSearch |
GCG |
Uses a profile to search a database. |
| profit |
EMBOSS |
Scan a sequence or database with a matrix or profile |
| rebaseextract |
EMBOSS |
Extract data from REBASE |
| Seg |
GCG |
Replaces low complexity regions in protein sequences with X characters. |
| SSearch |
GCG |
Smith-Waterman search of local GCG databases. |
| StringSearch |
GCG |
Identifies sequences by character patterns in the sequence documentation. |
| stssearch |
EMBOSS |
Searches a DNA sequence database with a set of STS primers and reports expected matches and
possible mismatches. A replacement for stssearch in the EGCG package. |
| TFastA |
GCG |
TFasta on local (translated nucleotide) GCG databases. |
| TFastX |
GCG |
As TFasta but allowing for frame shifts. |
| tfextract |
EMBOSS |
Extract data from TRANSFAC |
| Xnu |
GCG |
Masks tandem repeats in protein sequences with X characters. |
