| Program name | Description |
|---|---|
| cons | Creates a consensus from multiple alignments |
| megamerger | Merge two large overlapping nucleic acid sequences |
| merger | Merge two overlapping nucleic acid sequences |
| Program name | Description |
|---|---|
| diffseq | Find differences between nearly identical sequences |
| Program name | Description |
|---|---|
| dotmatcher | Displays a thresholded dotplot of two sequences |
| dotpath | Displays a non-overlapping wordmatch dotplot of two sequences |
| dottup | Displays a wordmatch dotplot of two sequences |
| polydot | Displays all-against-all dotplots of a set of sequences |
| Program name | Description |
|---|---|
| est2genome | Align EST and genomic DNA sequences |
| needle | Needleman-Wunsch global alignment |
| stretcher | Finds the best global alignment between two sequences |
| Program name | Description |
|---|---|
| matcher | Finds the best local alignments between two sequences |
| seqmatchall | Does an all-against-all comparison of a set of sequences |
| supermatcher | Finds a match of a large sequence against one or more sequences |
| water | Smith-Waterman local alignment |
| wordmatch | Finds all exact matches of a given size between 2 sequences |
| Program name | Description |
|---|---|
| emma | Multiple alignment program - interface to ClustalW program |
| infoalign | Information on a multiple sequence alignment |
| plotcon | Plots the quality of conservation of a sequence alignment |
| prettyplot | Displays aligned sequences, with colouring and boxing |
| showalign | Displays a multiple sequence alignment |
| tranalign | Align nucleic coding regions given the aligned proteins |
| Program name | Description |
|---|---|
| abiview | Reads ABI file and display the trace |
| cirdna | Draws circular maps of DNA constructs |
| lindna | Draws linear maps of DNA constructs |
| pepnet | Displays proteins as a helical net |
| pepwheel | Shows protein sequences as helices |
| prettyplot | Displays aligned sequences, with colouring and boxing |
| prettyseq | Output sequence with translated ranges |
| remap | Display a sequence with restriction cut sites, translation etc |
| seealso | Finds programs sharing group names |
| showalign | Displays a multiple sequence alignment |
| showdb | Displays information on the currently available databases |
| showfeat | Show features of a sequence |
| showseq | Display a sequence with features, translation etc |
| sixpack | Display a DNA sequence with 6-frame translation and ORFs |
| textsearch | Search sequence documentation text. SRS and Entrez are faster! |
| Program name | Description |
|---|---|
| biosed | Replace or delete sequence sections |
| cutseq | Removes a specified section from a sequence |
| degapseq | Removes gap characters from sequences |
| descseq | Alter the name or description of a sequence |
| entret | Reads and writes (returns) flatfile entries |
| extractfeat | Extract features from a sequence |
| extractseq | Extract regions from a sequence |
| listor | Writes a list file of the logical OR of two sets of sequences |
| maskfeat | Mask off features of a sequence |
| maskseq | Mask off regions of a sequence |
| newseq | Type in a short new sequence |
| noreturn | Removes carriage return from ASCII files |
| notseq | Excludes a set of sequences and writes out the remaining ones |
| nthseq | Writes one sequence from a multiple set of sequences |
| pasteseq | Insert one sequence into another |
| revseq | Reverse and complement a sequence |
| seqret | Reads and writes (returns) sequences |
| seqretsplit | Reads and writes (returns) sequences in individual files |
| skipseq | Reads and writes (returns) sequences, skipping the first few |
| splitter | Split a sequence into (overlapping) smaller sequences |
| trimest | Trim poly-A tails off EST sequences |
| trimseq | Trim ambiguous bits off the ends of sequences |
| union | Reads sequence fragments and builds one sequence |
| vectorstrip | Strips out DNA between a pair of vector sequences |
| yank | Reads a sequence range, appends the full USA to a list file |
| Program name | Description |
|---|---|
| findkm | Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot |
| Program name | Description |
|---|---|
| coderet | Extract CDS, mRNA and translations from feature tables |
| extractfeat | Extract features from a sequence |
| maskfeat | Mask off features of a sequence |
| showfeat | Show features of a sequence |
| twofeat | Finds neighbouring pairs of features in sequences |
| Program name | Description |
|---|---|
| infoalign | Information on a multiple sequence alignment |
| infoseq | Displays some simple information about sequences |
| seealso | Finds programs sharing group names |
| showdb | Displays information on the currently available databases |
| textsearch | Search sequence documentation text. SRS and Entrez are faster! |
| tfm | Displays a program's help documentation manual |
| whichdb | Search all databases for an entry |
| wossname | Finds programs by keywords in their one-line documentation |
| Program name | Description |
|---|---|
| einverted | Finds DNA inverted repeats |
| Program name | Description |
|---|---|
| cai | CAI codon adaptation index |
| chips | Codon usage statistics |
| codcmp | Codon usage table comparison |
| cusp | Create a codon usage table |
| syco | Synonymous codon usage Gribskov statistic plot |
| Program name | Description |
|---|---|
| banana | Bending and curvature plot in B-DNA |
| btwisted | Calculates the twisting in a B-DNA sequence |
| chaos | Create a chaos game representation plot for a sequence |
| compseq | Counts the composition of dimer/trimer/etc words in a sequence |
| dan | Calculates DNA RNA/DNA melting temperature |
| freak | Residue/base frequency table or plot |
| isochore | Plots isochores in large DNA sequences |
| sirna | Finds siRNA duplexes in mRNA |
| wordcount | Counts words of a specified size in a DNA sequence |
| Program name | Description |
|---|---|
| cpgplot | Plot CpG rich areas |
| cpgreport | Reports all CpG rich regions |
| geecee | Calculates the fractional GC content of nucleic acid sequences |
| newcpgreport | Report CpG rich areas |
| newcpgseek | Reports CpG rich regions |
| Program name | Description |
|---|---|
| getorf | Finds and extracts open reading frames (ORFs) |
| marscan | Finds MAR/SAR sites in nucleic sequences |
| plotorf | Plot potential open reading frames |
| showorf | Pretty output of DNA translations |
| sixpack | Display a DNA sequence with 6-frame translation and ORFs |
| syco | Synonymous codon usage Gribskov statistic plot |
| tcode | Fickett TESTCODE statistic to identify protein-coding DNA |
| wobble | Wobble base plot |
| Program name | Description |
|---|---|
| dreg | regular expression search of a nucleotide sequence |
| fuzznuc | Nucleic acid pattern search |
| fuzztran | Protein pattern search after translation |
| marscan | Finds MAR/SAR sites in nucleic sequences |
| Program name | Description |
|---|---|
| msbar | Mutate sequence beyond all recognition |
| shuffleseq | Shuffles a set of sequences maintaining composition |
| Program name | Description |
|---|---|
| eprimer3 | Picks PCR primers and hybridization oligos |
| primersearch | Searches DNA sequences for matches with primer pairs |
| stssearch | Searches a DNA database for matches with a set of STS primers |
| Program name | Description |
|---|---|
| profit | Scan a sequence or database with a matrix or profile |
| prophecy | Creates matrices/profiles from multiple alignments |
| prophet | Gapped alignment for profiles |
| Program name | Description |
|---|---|
| einverted | Finds DNA inverted repeats |
| equicktandem | Finds tandem repeats |
| etandem | Looks for tandem repeats in a nucleotide sequence |
| palindrome | Looks for inverted repeats in a nucleotide sequence |
| Program name | Description |
|---|---|
| recoder | Remove restriction sites but maintain the same translation |
| redata | Search REBASE for enzyme name, references, suppliers etc |
| remap | Display a sequence with restriction cut sites, translation etc |
| restover | Finds restriction enzymes that produce a specific overhang |
| restrict | Finds restriction enzyme cleavage sites |
| showseq | Display a sequence with features, translation etc |
| silent | Silent mutation restriction enzyme scan |
| Program name | Description |
|---|---|
| tfscan | Scans DNA sequences for transcription factors |
| Program name | Description |
|---|---|
| backtranseq | Back translate a protein sequence |
| coderet | Extract CDS, mRNA and translations from feature tables |
| plotorf | Plot potential open reading frames |
| prettyseq | Output sequence with translated ranges |
| remap | Display a sequence with restriction cut sites, translation etc |
| showorf | Pretty output of DNA translations |
| showseq | Display a sequence with features, translation etc |
| sixpack | Display a DNA sequence with 6-frame translation and ORFs |
| transeq | Translate nucleic acid sequences |
| Program name | Description |
|---|---|
| distmat | Creates a distance matrix from multiple alignments |
| Program name | Description |
|---|---|
| garnier | Predicts protein secondary structure |
| helixturnhelix | Report nucleic acid binding motifs |
| hmoment | Hydrophobic moment calculation |
| pepcoil | Predicts coiled coil regions |
| pepnet | Displays proteins as a helical net |
| pepwheel | Shows protein sequences as helices |
| tmap | Displays membrane spanning regions |
| Program name | Description |
|---|---|
| backtranseq | Back translate a protein sequence |
| charge | Protein charge plot |
| checktrans | Reports STOP codons and ORF statistics of a protein |
| compseq | Counts the composition of dimer/trimer/etc words in a sequence |
| emowse | Protein identification by mass spectrometry |
| freak | Residue/base frequency table or plot |
| iep | Calculates the isoelectric point of a protein |
| mwcontam | Shows molwts that match across a set of files |
| mwfilter | Filter noisy molwts from mass spec output |
| octanol | Displays protein hydropathy |
| pepinfo | Plots simple amino acid properties in parallel |
| pepstats | Protein statistics |
| pepwindow | Displays protein hydropathy |
| pepwindowall | Displays protein hydropathy of a set of sequences |
| Program name | Description |
|---|---|
| antigenic | Finds antigenic sites in proteins |
| digest | Protein proteolytic enzyme or reagent cleavage digest |
| epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
| fuzzpro | Protein pattern search |
| fuzztran | Protein pattern search after translation |
| helixturnhelix | Report nucleic acid binding motifs |
| oddcomp | Finds protein sequence regions with a biased composition |
| patmatdb | Search a protein sequence with a motif |
| patmatmotifs | Search a PROSITE motif database with a protein sequence |
| pepcoil | Predicts coiled coil regions |
| preg | Regular expression search of a protein sequence |
| pscan | Scans proteins using PRINTS |
| sigcleave | Reports protein signal cleavage sites |
| Program name | Description |
|---|---|
| msbar | Mutate sequence beyond all recognition |
| shuffleseq | Shuffles a set of sequences maintaining composition |
| Program name | Description |
|---|---|
| profit | Scan a sequence or database with a matrix or profile |
| prophecy | Creates matrices/profiles from multiple alignments |
| prophet | Gapped alignment for profiles |
| Program name | Description |
|---|---|
| aaindexextract | Extract data from AAINDEX |
| cutgextract | Extract data from CUTG |
| printsextract | Extract data from PRINTS |
| prosextract | Builds the PROSITE motif database for patmatmotifs to search |
| rebaseextract | Extract data from REBASE |
| tfextract | Extract data from TRANSFAC |
| Program name | Description |
|---|---|
| dbiblast | Index a BLAST database |
| dbifasta | Index a fasta database |
| dbiflat | Index a flat file database |
| dbigcg | Index a GCG formatted database |
| Program name | Description |
|---|---|
| embossdata | Finds or fetches the data files read in by the EMBOSS programs |
| embossversion | Writes the current EMBOSS version number |