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