|
Codon Usage |
| Program name | Source | Description |
|---|
| chips |
EMBOSS |
Codon usage statistics |
| codcmp |
EMBOSS |
Codon usage table comparison |
| CodonFrequency |
GCG |
Tabulates the codon frequency in sequences |
| CodonPreference |
GCG |
Gene finder based on codon frequency |
| Correspond
| GCG |
Compares patterns of codon usage. |
| cusp |
EMBOSS |
Create a codon usage table |
| nip4 |
Staden |
Analyses nucleotide sequences to find genes, restriction sites and motifs. It will perform
translations, find ORFs and examine codon usage. |
| syco |
EMBOSS |
Synonymous codon usage Gribskov statistic plot |
| TestCode |
GCG |
Identify potential protein coding regions by non-random third base composition. |
|
CpG |
| Program name | Source | Description |
|---|
| cpgplot |
EMBOSS |
Plot CpG rich areas |
| cpgreport |
EMBOSS |
Reports CpG rich regions |
| geecee |
EMBOSS |
Calculates the fractional GC content of a nucleic acid sequence |
| newcpgreport |
EMBOSS |
Report CpG rich areas |
| newcpgseek |
EMBOSS |
Reports CpG rich regions |
|
Motif Based |
| 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. |
| nip4 |
Staden |
Analyses nucleotide sequences to find genes, restriction sites and motifs. It will perform
translations, find ORFs and examine codon usage. |
| Terminator |
GCG |
Searches for prokaryotic factor-independent RNA polymerase terminators. |
| tfscan |
EMBOSS |
Scans DNA sequences for transcription factors. |
|
Others |
| Program name | Source | Description |
|---|
| est2genome |
EMBOSS |
Align EST and genomic DNA sequences |
