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Single Sequence Analysis |
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Please note that several programs of this type have been placed in other groups. Codon usage programs are under "Gene Finding"; motif searches are under "Pattern Finding"; protein secondary structure and hydrophobicity are under "Protein Features"; and restriction enzyme analyses are under "Maps and Digests". |
| Sequence Composition | DNA/RNA repeats | Shuffling sequences |
| Isoelectric point | DNA properties | Others |
| See also: | The Software List | Software by Group | I Want To... |
| Gene Finding | Pattern Matching | Protein Features | Maps and Digests |
| Sequence Composition | ||
| Program name | Source | Description |
|---|---|---|
| aacomp | FastA | Calculates the amino acid composition and molecular weight of a sequence. |
| chips | EMBOSS | Codon usage statistics |
| CodonFrequency | GCG | Tabulates the codon frequency in sequences |
| Composition | GCG | Determines the nucleic/amino acid composition of sequences |
| compseq | EMBOSS | Counts the composition of dimer/trimer/etc words in a sequence |
| cusp | EMBOSS | Create a codon usage table |
| geecee | EMBOSS | Calculates the fractional GC content of a nucleic acid sequence |
| wordcount | EMBOSS | Counts words of a specified size in a DNA sequence. |
| DNA/RNA Repeats | ||
| Program name | Source | Description |
| einverted | EMBOSS | Finds DNA inverted repeats |
| equicktandem | EMBOSS | Finds tandem repeats |
| etandem | EMBOSS | Looks for tandem repeats in a nucleotide sequence. |
| palindrome | EMBOSS | Looks for inverted repeats in a nucleotide sequence. |
| Repeat | GCG | Finds direct repeats in sequences. |
| Stemloop | GCG | Finds stems (inverted repeats) within a sequence. |
| Shuffling and Altering Sequences | ||
| Program name | Source | Description |
| crandseq | FastA | Produces a randomly shuffled DNA sequence keeping the codons intact. |
| randseq | FastA | Produces a randomly shuffled sequence from a query sequence. |
| Shuffle | GCG | Randomizes the order of a sequence without changing the composition. |
| shuffleseq | EMBOSS | Shuffles a set of sequences maintaining composition |
| Simplify | GCG | Reduces the number of symbols in a sequence based on similar properties. |
| Isoelectric Point | ||
| Program name | Source | Description |
| iep | EMBOSS | Calculates the isoelectric point of a protein |
| Isoelectric | GCG | Plots charge as a function of pH for a peptide sequence. |
| pepstats | EMBOSS | Protein statistics such as isoelectric point and molecular weight |
| DNA Properties | ||
| Program name | Source | Description |
| banana | EMBOSS | Bending and Curvature Plot in B-DNA |
| dan | EMBOSS | Plot melting temperatures for DNA. |
| Others | ||
| Program name | Source | Description |
| bestscor | FastA | Calculates the best self-comparison score. |
| chaos | EMBOSS | Create a chaos plot for a sequence. |
| complex | EMBOSS | Find the linguistic complexity in nucleotide sequences |
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