|
Patterns and Motifs |
| Program name | Source | Description |
|---|
| FindPatterns |
GCG |
Searches for short patterns in sequences. |
| fuzznuc |
EMBOSS |
Nucleic acid pattern search |
| fuzzpro |
EMBOSS |
Protein pattern search |
| Motifs |
GCG |
Searches for ProSite patterns in a sequence. |
| MotifSearch |
GCG |
Searches a set of sequences with a profile. |
| nip4 |
Staden |
Analyses nucleotide sequences to find genes, restriction sites and motifs. It will perform
translations, find ORFs and examine codon usage. |
| patmatdb |
EMBOSS |
Matching a Prosite motif against a Protein Sequence Database. |
| patmatmotifs |
EMBOSS |
Compares a protein sequence to the PROSITE motif database. |
| pscan |
EMBOSS |
Locates fingerprints (multiple motif features) in a protein sequence. |
| Window |
GCG |
Makes a table of the frequencies of sequence patterns within a window along a sequence. |
|
Consensus Sequences |
| Program name | Source | Description |
|---|
| Consensus |
GCG |
Generates a consensus sequence for short nucleotide sequences. |
| FitConsensus |
GCG |
Finds matches to a consensus sequence matrix. |
| MEME |
GCG |
Finds conserved motifs in a group of unaligned sequences. |
| tfscan |
EMBOSS |
Scans DNA sequences for transcription factors. |
