Soaplab Web Services at Vital-IT
[Soaplab version: 2.2.0, build: Thu Aug 5 14:59:40 CEST 2010]
List of WSDL files for programmatic access
List of WSDL files for programmatic access
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Soaplab Web Services at Vital-IT
[Soaplab version: 2.2.0, build: Thu Aug 5 14:59:40 CEST 2010]
List of WSDL files for programmatic access |
|
| Category | Service name | Description |
|---|---|---|
| Alignment consensus | ||
| cons (WSDL) | Create a consensus sequence from a multiple alignment | |
| consambig (WSDL) | Create an ambiguous consensus sequence from a multiple alignment | |
| megamerger (WSDL) | Merge two large overlapping DNA sequences | |
| merger (WSDL) | Merge two overlapping sequences | |
| Alignment differences | ||
| diffseq (WSDL) | Compare and report features of two similar sequences | |
| Alignment dot plots | ||
| dotmatcher (WSDL) | Draw a threshold dotplot of two sequences | |
| dotpath (WSDL) | Draw a non-overlapping wordmatch dotplot of two sequences | |
| dottup (WSDL) | Displays a wordmatch dotplot of two sequences | |
| polydot (WSDL) | Draw dotplots for all-against-all comparison of a sequence set | |
| Alignment global | ||
| esim4 (WSDL) | Align an mRNA to a genomic DNA sequence | |
| est2genome (WSDL) | Align EST sequences to genomic DNA sequence | |
| ggsearch (WSDL) | GGSEARCH - global alignments (Needleman-Wunsch) | |
| glsearch (WSDL) | GLSEARCH - query global vs. target local alignments | |
| needle (WSDL) | Needleman-Wunsch global alignment of two sequences | |
| stretcher (WSDL) | Needleman-Wunsch rapid global alignment of two sequences | |
| Alignment local | ||
| glsearch (WSDL) | GLSEARCH - query global vs. target local alignments | |
| lalign (WSDL) | LALIGN - find multiple matching subsegments in two sequences | |
| matcher (WSDL) | Waterman-Eggert local alignment of two sequences | |
| prss (WSDL) | PRSS Optimal score of an alignment | |
| seqmatchall (WSDL) | All-against-all word comparison of a sequence set | |
| supermatcher (WSDL) | Calculate approximate local pair-wise alignments of larger sequences | |
| water (WSDL) | Smith-Waterman local alignment of sequences | |
| wordfinder (WSDL) | Match large sequences against one or more other sequences | |
| wordmatch (WSDL) | Finds regions of identity (exact matches) of two sequences | |
| Alignment multiple | ||
| clustalw (WSDL) | ClustalW: multiple alignment program for DNA or proteins | |
| clustalw_simple (WSDL) | ClustalW: multiple alignment program for DNA or proteins | |
| edialign (WSDL) | Local multiple alignment of sequences | |
| emma (WSDL) | Multiple sequence alignment (ClustalW wrapper) | |
| infoalign (WSDL) | Display basic information about a multiple sequence alignment | |
| mafft (WSDL) | MAFFT: Multiple alignment program for aa or nt sequences | |
| mafft_simple (WSDL) | MAFFT: Multiple alignment program for aa or nt sequences | |
| plotcon (WSDL) | Plot conservation of a sequence alignment | |
| prettyplot (WSDL) | Draw a sequence alignment with pretty formatting | |
| showalign (WSDL) | Display a multiple sequence alignment in pretty format | |
| tranalign (WSDL) | Generate an alignment of nucleic coding regions from aligned proteins | |
| Assembly fragment assembly | ||
| emira (WSDL) | MIRA fragment assembly program | |
| emiraest (WSDL) | MIRAest fragment assembly program | |
| Database query | ||
| fetch (WSDL) | Fetch get sequences | |
| randomseqfromunimes (WSDL) | Get a random sequence from UniMes | |
| Display | ||
| cirdna (WSDL) | Draws circular maps of DNA constructs | |
| lindna (WSDL) | Draws linear maps of DNA constructs | |
| pepnet (WSDL) | Draw a helical net for a protein sequence | |
| pepwheel (WSDL) | Draw a helical wheel diagram for a protein sequence | |
| prettyplot (WSDL) | Draw a sequence alignment with pretty formatting | |
| prettyseq (WSDL) | Write a nucleotide sequence and its translation to file | |
| remap (WSDL) | Display restriction enzyme binding sites in a nucleotide sequence | |
| seealso (WSDL) | Finds programs with similar function to a specified program | |
| showalign (WSDL) | Display a multiple sequence alignment in pretty format | |
| showdb (WSDL) | Displays information on configured databases | |
| showfeat (WSDL) | Display features of a sequence in pretty format | |
| showpep (WSDL) | Displays protein sequences with features in pretty format | |
| showseq (WSDL) | Displays sequences with features in pretty format | |
| sixpack (WSDL) | Display a DNA sequence with 6-frame translation and ORFs | |
| textsearch (WSDL) | Search the textual description of sequence(s) | |
| Ebi alignment | ||
| wu_blastn_raw (WSDL) | WU-BLAST with output in TXT format | |
| wu_blastn_xml (WSDL) | WU-BLAST with output in XML format | |
| wu_blastp_raw (WSDL) | WU-BLAST with output in TXT format | |
| wu_blastp_xml (WSDL) | WU-BLAST with output in XML format | |
| wu_blastx_raw (WSDL) | WU-BLAST with output in TXT format | |
| wu_blastx_xml (WSDL) | WU-BLAST with output in XML format | |
| wu_tblastn_raw (WSDL) | WU-BLAST with output in TXT format | |
| wu_tblastn_xml (WSDL) | WU-BLAST with output in XML format | |
| wu_tblastx_raw (WSDL) | WU-BLAST with output in TXT format | |
| wu_tblastx_xml (WSDL) | WU-BLAST with output in XML format | |
| Ebi interproscan | ||
| proteinraw (WSDL) | InterProScan with output in TXT format | |
| proteinxml (WSDL) | InterProScan with output in XML | |
| Ebi similarity search | ||
| fasta_dna_raw (WSDL) | FASTA with output in TXT format | |
| fasta_dna_xml (WSDL) | FASTA with output in XML format | |
| fasta_protein_raw (WSDL) | FASTA with output in TXT format | |
| fasta_protein_xml (WSDL) | FASTA with output in XML format | |
| Edit | ||
| aligncopy (WSDL) | Reads and writes alignments | |
| aligncopypair (WSDL) | Reads and writes pairs from alignments | |
| biosed (WSDL) | Replace or delete sequence sections | |
| codcopy (WSDL) | Copy and reformat a codon usage table | |
| cutseq (WSDL) | Removes a section from a sequence | |
| degapseq (WSDL) | Removes non-alphabetic (e.g. gap) characters from sequences | |
| descseq (WSDL) | Alter the name or description of a sequence. | |
| entret (WSDL) | Retrieves sequence entries from flatfile databases and files | |
| extractalign (WSDL) | Extract regions from a sequence alignment | |
| extractfeat (WSDL) | Extract features from sequence(s) | |
| extractseq (WSDL) | Extract regions from a sequence | |
| featcopy (WSDL) | Reads and writes a feature table | |
| featreport (WSDL) | Reads and writes a feature table | |
| listor (WSDL) | Write a list file of the logical OR of two sets of sequences | |
| makenucseq (WSDL) | Create random nucleotide sequences | |
| makeprotseq (WSDL) | Create random protein sequences | |
| maskambignuc (WSDL) | Masks all ambiguity characters in nucleotide sequences with N | |
| maskambigprot (WSDL) | Masks all ambiguity characters in protein sequences with X | |
| maskfeat (WSDL) | Write a sequence with masked features | |
| maskseq (WSDL) | Write a sequence with masked regions | |
| newseq (WSDL) | Create a sequence file from a typed-in sequence | |
| nohtml (WSDL) | Remove mark-up (e.g. HTML tags) from an ASCII text file | |
| noreturn (WSDL) | Remove carriage return from ASCII files | |
| nospace (WSDL) | Remove all whitespace from an ASCII text file | |
| notab (WSDL) | Replace tabs with spaces in an ASCII text file | |
| notseq (WSDL) | Write to file a subset of an input stream of sequences | |
| nthseq (WSDL) | Write to file a single sequence from an input stream of sequences | |
| nthseqset (WSDL) | Reads and writes (returns) one set of sequences from many | |
| pasteseq (WSDL) | Insert one sequence into another | |
| readseq (WSDL) | ReadSeq reads and reformats biosequences | |
| readseq_simple (WSDL) | ReadSeq reads and reformats biosequences | |
| revseq (WSDL) | Reverse and complement a nucleotide sequence | |
| seqret (WSDL) | Reads and writes (returns) sequences | |
| seqretsetall (WSDL) | Reads and writes (returns) many sets of sequences | |
| sizeseq (WSDL) | Sort sequences by size | |
| skipredundant (WSDL) | Remove redundant sequences from an input set | |
| skipseq (WSDL) | Reads and writes (returns) sequences | |
| splitsource (WSDL) | Split sequence(s) into original source sequences | |
| splitter (WSDL) | Split sequence(s) into smaller sequences | |
| trimest (WSDL) | Remove poly-A tails from nucleotide sequences | |
| trimseq (WSDL) | Remove unwanted characters from start and end of sequence(s) | |
| trimspace (WSDL) | Remove extra whitespace from an ASCII text file | |
| union (WSDL) | Concatenate multiple sequences into a single sequence | |
| vectorstrip (WSDL) | Removes vectors from the ends of nucleotide sequence(s) | |
| yank (WSDL) | Add a sequence reference (a full USA) to a list file | |
| Embnet | ||
| blastn (WSDL) | BLASTn finds regions of similarity between a nucleotide query sequence and a nucleotide sequence database | |
| blastn_simple (WSDL) | BLASTn finds regions of similarity between a nucleotide query sequence and a nucleotide sequence database | |
| blastp (WSDL) | BLASTp finds regions of similarity between an amino acid query sequence and a protein sequence database | |
| blastp_simple (WSDL) | BLASTp finds regions of similarity between an amino acid query sequence and a protein sequence database | |
| blastx (WSDL) | BLASTx finds regions of similarity between a nucleotide query sequence translated in all reading frames and a protein sequence database | |
| blastx_simple (WSDL) | BLASTx finds regions of similarity between a nucleotide query sequence translated in all reading frames and a protein sequence database | |
| clustalw (WSDL) | ClustalW: multiple alignment program for DNA or proteins | |
| clustalw_simple (WSDL) | ClustalW: multiple alignment program for DNA or proteins | |
| coils (WSDL) | COILS - Coiled-coil domains prediction | |
| csblast (WSDL) | CS-BLAST finds regions of low similarity between peptides (Tuned Position-Specific Iterated BLAST) | |
| csblast_simple (WSDL) | CS-BLAST finds regions of low similarity between peptides (Tuned Position-Specific Iterated BLAST) | |
| estscan2 (WSDL) | ESTScan detects coding regions in DNA sequences | |
| fetch (WSDL) | Fetch get sequences | |
| ggsearch (WSDL) | GGSEARCH - global alignments (Needleman-Wunsch) | |
| glsearch (WSDL) | GLSEARCH - query global vs. target local alignments | |
| ipcr (WSDL) | IPCR: Virtual PCR tool | |
| lalign (WSDL) | LALIGN - find multiple matching subsegments in two sequences | |
| mafft (WSDL) | MAFFT: Multiple alignment program for aa or nt sequences | |
| mafft_simple (WSDL) | MAFFT: Multiple alignment program for aa or nt sequences | |
| megablast (WSDL) | megaBLAST finds regions of high similarity between a nucleotide query sequence and a nucleotide sequence database | |
| megablast_simple (WSDL) | megaBLAST finds regions of high similarity between a nucleotide query sequence and a nucleotide sequence database | |
| prss (WSDL) | PRSS Optimal score of an alignment | |
| psiblast (WSDL) | psiBLAST finds regions of low similarity between peptides (Position-Specific Iterated BLAST) | |
| psiblast_simple (WSDL) | psiBLAST finds regions of low similarity between peptides (Position-Specific Iterated BLAST) | |
| randomseqfromunimes (WSDL) | Get a random sequence from UniMes | |
| readseq (WSDL) | ReadSeq reads and reformats biosequences | |
| readseq_simple (WSDL) | ReadSeq reads and reformats biosequences | |
| tblastn (WSDL) | tBLASTn finds regions of similarity between a protein query sequence and a nucleotide sequence database dynamically translated in all reading frames | |
| tblastn_simple (WSDL) | tBLASTn finds regions of similarity between a protein query sequence and a nucleotide sequence database dynamically translated in all reading frames | |
| tblastx (WSDL) | tBLASTx finds regions of similarity between the six-frame translations of a nucleotide query sequence and the six-frame translations of a nucleotide sequence database | |
| tblastx_simple (WSDL) | tBLASTx finds regions of similarity between the six-frame translations of a nucleotide query sequence and the six-frame translations of a nucleotide sequence database | |
| tmpred (WSDL) | Prediction of Transmembrane Regions and Orientation | |
| Enzyme kinetics | ||
| findkm (WSDL) | Calculate and plot enzyme reaction data | |
| Feature tables | ||
| coderet (WSDL) | Extract CDS | |
| extractfeat (WSDL) | Extract features from sequence(s) | |
| maskfeat (WSDL) | Write a sequence with masked features | |
| showfeat (WSDL) | Display features of a sequence in pretty format | |
| twofeat (WSDL) | Finds neighbouring pairs of features in sequence(s) | |
| Hmm | ||
| ehmmalign (WSDL) | Align sequences to an HMM profile | |
| ehmmbuild (WSDL) | Build a profile HMM from an alignment. | |
| ehmmcalibrate (WSDL) | Calibrate HMM search statistics | |
| ehmmconvert (WSDL) | Convert between profile HMM file formats | |
| ehmmemit (WSDL) | Generate sequences from a profile HMM. | |
| ehmmfetch (WSDL) | Retrieve an HMM from an HMM database. | |
| ehmmindex (WSDL) | Create a binary SSI index for an HMM database. | |
| ehmmpfam (WSDL) | Search one or more sequences against an HMM database. | |
| ehmmsearch (WSDL) | Search a sequence database with a profile HMM | |
| Information | ||
| infoalign (WSDL) | Display basic information about a multiple sequence alignment | |
| infobase (WSDL) | Return information on a given nucleotide base | |
| inforesidue (WSDL) | Return information on a given amino acid residue | |
| infoseq (WSDL) | Display basic information about sequences | |
| seealso (WSDL) | Finds programs with similar function to a specified program | |
| showdb (WSDL) | Displays information on configured databases | |
| textsearch (WSDL) | Search the textual description of sequence(s) | |
| tfm (WSDL) | Displays full documentation for an application | |
| whichdb (WSDL) | Search all sequence databases for an entry and retrieve it | |
| wossname (WSDL) | Finds programs by keywords in their short description | |
| Interproscan | ||
| proteinraw (WSDL) | InterProScan with output in TXT format | |
| proteinxml (WSDL) | InterProScan with output in XML | |
| Nucleic 2d structure | ||
| einverted (WSDL) | Finds inverted repeats in nucleotide sequences | |
| vrnaalifold (WSDL) | RNA alignment folding | |
| vrnaalifoldpf (WSDL) | RNA alignment folding with partition | |
| vrnacofold (WSDL) | RNA cofolding | |
| vrnacofoldconc (WSDL) | RNA cofolding with concentrations | |
| vrnacofoldpf (WSDL) | RNA cofolding with partitioning | |
| vrnadistance (WSDL) | RNA distances | |
| vrnaduplex (WSDL) | RNA duplex calculation | |
| vrnaeval (WSDL) | RNA eval | |
| vrnaevalpair (WSDL) | RNA eval with cofold | |
| vrnafold (WSDL) | Calculate secondary structures of RNAs | |
| vrnafoldpf (WSDL) | Secondary structures of RNAs with partition | |
| vrnaheat (WSDL) | RNA melting | |
| vrnainverse (WSDL) | RNA sequences matching a structure | |
| vrnalfold (WSDL) | Calculate locally stable secondary structures of RNAs | |
| vrnaplot (WSDL) | Plot vrnafold output | |
| vrnasubopt (WSDL) | Calculate RNA suboptimals | |
| Nucleic codon usage | ||
| cai (WSDL) | Calculate codon adaptation index | |
| chips (WSDL) | Calculates Nc codon usage statistic | |
| codcmp (WSDL) | Codon usage table comparison | |
| cusp (WSDL) | Create a codon usage table from nucleotide sequence(s) | |
| syco (WSDL) | Draw synonymous codon usage statictic plot for a nucleotide sequence | |
| Nucleic composition | ||
| banana (WSDL) | Plot bending and curvature data for B-DNA | |
| btwisted (WSDL) | Calculate the twisting in a B-DNA sequence | |
| chaos (WSDL) | Draw a chaos game representation plot for a nucleotide sequence | |
| compseq (WSDL) | Calculate the composition of unique words in sequences | |
| dan (WSDL) | Calculates nucleic acid melting temperature | |
| density (WSDL) | Draw a nucleic acid density plot | |
| freak (WSDL) | Generate residue/base frequency table or plot | |
| isochore (WSDL) | Plots isochores in DNA sequences | |
| sirna (WSDL) | Finds siRNA duplexes in mRNA | |
| wordcount (WSDL) | Count and extract unique words in DNA sequence(s) | |
| Nucleic cpg islands | ||
| cpgplot (WSDL) | Identify and plot CpG islands in nucleotide sequence(s) | |
| cpgreport (WSDL) | Identify and report CpG-rich regions in nucleotide sequence(s) | |
| geecee (WSDL) | Calculate fractional GC content of nucleic acid sequences | |
| newcpgreport (WSDL) | Identify CpG islands in nucleotide sequence(s) | |
| newcpgseek (WSDL) | Identify and report CpG-rich regions in nucleotide sequence(s) | |
| Nucleic gene finding | ||
| estscan2 (WSDL) | ESTScan detects coding regions in DNA sequences | |
| getorf (WSDL) | Finds and extracts open reading frames (ORFs) | |
| marscan (WSDL) | Finds matrix/scaffold recognition (MRS) signatures in DNA sequences | |
| plotorf (WSDL) | Plot potential open reading frames in a nucleotide sequence | |
| showorf (WSDL) | Display a nucleotide sequence and translation in pretty format | |
| sixpack (WSDL) | Display a DNA sequence with 6-frame translation and ORFs | |
| syco (WSDL) | Draw synonymous codon usage statictic plot for a nucleotide sequence | |
| tcode (WSDL) | Identify protein-coding regions using Fickett TESTCODE statistic | |
| wobble (WSDL) | Plot third base position variability in a nucleotide sequence | |
| Nucleic motifs | ||
| dreg (WSDL) | Regular expression search of nucleotide sequence(s) | |
| fuzznuc (WSDL) | Search for patterns in nucleotide sequences | |
| fuzztran (WSDL) | Search for patterns in protein sequences (translated) | |
| marscan (WSDL) | Finds matrix/scaffold recognition (MRS) signatures in DNA sequences | |
| Nucleic mutation | ||
| msbar (WSDL) | Mutate a sequence | |
| shuffleseq (WSDL) | Shuffles a set of sequences maintaining composition | |
| Nucleic primers | ||
| eprimer3 (WSDL) | Picks PCR primers and hybridization oligos | |
| ipcr (WSDL) | IPCR: Virtual PCR tool | |
| primersearch (WSDL) | Search DNA sequences for matches with primer pairs | |
| stssearch (WSDL) | Search a DNA database for matches with a set of STS primers | |
| Nucleic profiles | ||
| profit (WSDL) | Scan one or more sequences with a simple frequency matrix | |
| prophecy (WSDL) | Create frequency matrix or profile from a multiple alignment | |
| prophet (WSDL) | Scan one or more sequences with a Gribskov or Henikoff profile | |
| Nucleic repeats | ||
| einverted (WSDL) | Finds inverted repeats in nucleotide sequences | |
| equicktandem (WSDL) | Finds tandem repeats in nucleotide sequences | |
| etandem (WSDL) | Finds tandem repeats in a nucleotide sequence | |
| palindrome (WSDL) | Finds inverted repeats in nucleotide sequence(s) | |
| Nucleic restriction | ||
| recoder (WSDL) | Find restriction sites to remove (mutate) with no translation change | |
| redata (WSDL) | Retrieve information from REBASE restriction enzyme database | |
| remap (WSDL) | Display restriction enzyme binding sites in a nucleotide sequence | |
| restover (WSDL) | Find restriction enzymes producing a specific overhang | |
| restrict (WSDL) | Report restriction enzyme cleavage sites in a nucleotide sequence | |
| showseq (WSDL) | Displays sequences with features in pretty format | |
| silent (WSDL) | Find restriction sites to insert (mutate) with no translation change | |
| Nucleic rna folding | ||
| vrnaalifold (WSDL) | RNA alignment folding | |
| vrnaalifoldpf (WSDL) | RNA alignment folding with partition | |
| vrnacofold (WSDL) | RNA cofolding | |
| vrnacofoldconc (WSDL) | RNA cofolding with concentrations | |
| vrnacofoldpf (WSDL) | RNA cofolding with partitioning | |
| vrnadistance (WSDL) | RNA distances | |
| vrnaduplex (WSDL) | RNA duplex calculation | |
| vrnaeval (WSDL) | RNA eval | |
| vrnaevalpair (WSDL) | RNA eval with cofold | |
| vrnafold (WSDL) | Calculate secondary structures of RNAs | |
| vrnafoldpf (WSDL) | Secondary structures of RNAs with partition | |
| vrnaheat (WSDL) | RNA melting | |
| vrnainverse (WSDL) | RNA sequences matching a structure | |
| vrnalfold (WSDL) | Calculate locally stable secondary structures of RNAs | |
| vrnaplot (WSDL) | Plot vrnafold output | |
| vrnasubopt (WSDL) | Calculate RNA suboptimals | |
| Nucleic transcription | ||
| jaspscan (WSDL) | Scans DNA sequences for transcription factors | |
| tfscan (WSDL) | Identify transcription factor binding sites in DNA sequences | |
| Nucleic translation | ||
| backtranambig (WSDL) | Back-translate a protein sequence to ambiguous nucleotide sequence | |
| backtranseq (WSDL) | Back-translate a protein sequence to a nucleotide sequence | |
| coderet (WSDL) | Extract CDS | |
| plotorf (WSDL) | Plot potential open reading frames in a nucleotide sequence | |
| prettyseq (WSDL) | Write a nucleotide sequence and its translation to file | |
| remap (WSDL) | Display restriction enzyme binding sites in a nucleotide sequence | |
| showorf (WSDL) | Display a nucleotide sequence and translation in pretty format | |
| showseq (WSDL) | Displays sequences with features in pretty format | |
| sixpack (WSDL) | Display a DNA sequence with 6-frame translation and ORFs | |
| transeq (WSDL) | Translate nucleic acid sequences | |
| Phylogeny consensus | ||
| fconsense (WSDL) | Majority-rule and strict consensus tree | |
| ftreedist (WSDL) | Distances between trees | |
| ftreedistpair (WSDL) | Distances between two sets of trees | |
| Phylogeny continuous characters | ||
| fcontrast (WSDL) | Continuous character Contrasts | |
| Phylogeny discrete characters | ||
| fclique (WSDL) | Largest clique program | |
| fdollop (WSDL) | Dollo and polymorphism parsimony algorithm | |
| fdolpenny (WSDL) | Penny algorithm Dollo or polymorphism | |
| ffactor (WSDL) | Multistate to binary recoding program | |
| fmix (WSDL) | Mixed parsimony algorithm | |
| fpars (WSDL) | Discrete character parsimony | |
| fpenny (WSDL) | Penny algorithm | |
| Phylogeny distance matrix | ||
| ffitch (WSDL) | Fitch-Margoliash and Least-Squares Distance Methods | |
| fkitsch (WSDL) | Fitch-Margoliash method with contemporary tips | |
| fneighbor (WSDL) | Phylogenies from distance matrix by N-J or UPGMA method | |
| Phylogeny gene frequencies | ||
| fcontml (WSDL) | Gene frequency and continuous character Maximum Likelihood | |
| fgendist (WSDL) | Compute genetic distances from gene frequencies | |
| Phylogeny molecular sequence | ||
| distmat (WSDL) | Create a distance matrix from a multiple sequence alignment | |
| fdiscboot (WSDL) | Bootstrapped discrete sites algorithm | |
| fdnacomp (WSDL) | DNA compatibility algorithm | |
| fdnadist (WSDL) | Nucleic acid sequence Distance Matrix program | |
| fdnainvar (WSDL) | Nucleic acid sequence Invariants method | |
| fdnaml (WSDL) | Estimates nucleotide phylogeny by maximum likelihood | |
| fdnamlk (WSDL) | Estimates nucleotide phylogeny by maximum likelihood | |
| fdnapars (WSDL) | DNA parsimony algorithm | |
| fdnapenny (WSDL) | Penny algorithm for DNA | |
| ffreqboot (WSDL) | Bootstrapped genetic frequencies algorithm | |
| fproml (WSDL) | Protein phylogeny by maximum likelihood | |
| fpromlk (WSDL) | Protein phylogeny by maximum likelihood | |
| fprotdist (WSDL) | Protein distance algorithm | |
| fprotpars (WSDL) | Protein parsimony algorithm | |
| frestboot (WSDL) | Bootstrapped restriction sites algorithm | |
| frestdist (WSDL) | Distance matrix from restriction sites or fragments | |
| frestml (WSDL) | Restriction site maximum Likelihood method | |
| fseqboot (WSDL) | Bootstrapped sequences algorithm | |
| fseqbootall (WSDL) | Bootstrapped sequences algorithm | |
| Phylogeny tree drawing | ||
| fdrawgram (WSDL) | Plots a cladogram- or phenogram-like rooted tree diagram | |
| fdrawtree (WSDL) | Plots an unrooted tree diagram | |
| Protein 2d structure | ||
| coils (WSDL) | COILS - Coiled-coil domains prediction | |
| garnier (WSDL) | Predicts protein secondary structure using GOR method | |
| helixturnhelix (WSDL) | Identify nucleic acid-binding motifs in protein sequences | |
| hmoment (WSDL) | Calculate and plot hydrophobic moment for protein sequence(s) | |
| pepcoil (WSDL) | Predicts coiled coil regions in protein sequences | |
| pepnet (WSDL) | Draw a helical net for a protein sequence | |
| pepwheel (WSDL) | Draw a helical wheel diagram for a protein sequence | |
| tmap (WSDL) | Predict and plot transmembrane segments in protein sequences | |
| tmpred (WSDL) | Prediction of Transmembrane Regions and Orientation | |
| topo (WSDL) | Draws an image of a transmembrane protein | |
| Protein 3d structure | ||
| domainrep (WSDL) | Reorder DCF file to identify representative structures. | |
| psiphi (WSDL) | Calculates phi and psi torsion angles from protein coordinates | |
| rocon (WSDL) | Generates a hits file from comparing two DHF files | |
| seqwords (WSDL) | Generates DHF files from keyword search of UniProt. | |
| sigscan (WSDL) | Generates hits (DHF file) from a signature search | |
| sos (WSDL) | SoS - SNPs mapping onto Structures | |
| Protein composition | ||
| backtranambig (WSDL) | Back-translate a protein sequence to ambiguous nucleotide sequence | |
| backtranseq (WSDL) | Back-translate a protein sequence to a nucleotide sequence | |
| charge (WSDL) | Draw a protein charge plot | |
| checktrans (WSDL) | Reports STOP codons and ORF statistics of a protein | |
| compseq (WSDL) | Calculate the composition of unique words in sequences | |
| emowse (WSDL) | Search protein sequences by digest fragment molecular weight | |
| freak (WSDL) | Generate residue/base frequency table or plot | |
| iep (WSDL) | Calculate the isoelectric point of proteins | |
| mwcontam (WSDL) | Find weights common to multiple molecular weights files | |
| mwfilter (WSDL) | Filter noisy data from molecular weights file | |
| octanol (WSDL) | Draw a White-Wimley protein hydropathy plot | |
| pepinfo (WSDL) | Plot amino acid properties of a protein sequence in parallel. | |
| pepstats (WSDL) | Calculates statistics of protein properties | |
| pepwindow (WSDL) | Draw a hydropathy plot for a protein sequence | |
| pepwindowall (WSDL) | Draw Kyte-Doolittle hydropathy plot for a protein alignment | |
| wordcount (WSDL) | Count and extract unique words in DNA sequence(s) | |
| Protein motifs | ||
| antigenic (WSDL) | Finds antigenic sites in proteins | |
| digest (WSDL) | Reports on protein proteolytic enzyme or reagent cleavage sites | |
| emast (WSDL) | Motif detection | |
| ememe (WSDL) | Multiple EM for Motif Elicitation | |
| ememetext (WSDL) | Multiple EM for Motif Elicitation. Text file only. | |
| epestfind (WSDL) | Finds PEST motifs as potential proteolytic cleavage sites | |
| fuzzpro (WSDL) | Search for patterns in protein sequences | |
| fuzztran (WSDL) | Search for patterns in protein sequences (translated) | |
| helixturnhelix (WSDL) | Identify nucleic acid-binding motifs in protein sequences | |
| oddcomp (WSDL) | Identify proteins with specified sequence word composition | |
| patmatdb (WSDL) | Searches protein sequences with a sequence motif | |
| patmatmotifs (WSDL) | Scan a protein sequence with motifs from the PROSITE database | |
| pepcoil (WSDL) | Predicts coiled coil regions in protein sequences | |
| preg (WSDL) | Regular expression search of protein sequence(s) | |
| pscan (WSDL) | Scans protein sequence(s) with fingerprints from the PRINTS database | |
| sigcleave (WSDL) | Reports on signal cleavage sites in a protein sequence | |
| Protein mutation | ||
| msbar (WSDL) | Mutate a sequence | |
| shuffleseq (WSDL) | Shuffles a set of sequences maintaining composition | |
| Protein profiles | ||
| profit (WSDL) | Scan one or more sequences with a simple frequency matrix | |
| prophecy (WSDL) | Create frequency matrix or profile from a multiple alignment | |
| prophet (WSDL) | Scan one or more sequences with a Gribskov or Henikoff profile | |
| Similarity | ||
| blastn (WSDL) | BLASTn finds regions of similarity between a nucleotide query sequence and a nucleotide sequence database | |
| blastn_simple (WSDL) | BLASTn finds regions of similarity between a nucleotide query sequence and a nucleotide sequence database | |
| blastp (WSDL) | BLASTp finds regions of similarity between an amino acid query sequence and a protein sequence database | |
| blastp_simple (WSDL) | BLASTp finds regions of similarity between an amino acid query sequence and a protein sequence database | |
| blastx (WSDL) | BLASTx finds regions of similarity between a nucleotide query sequence translated in all reading frames and a protein sequence database | |
| blastx_simple (WSDL) | BLASTx finds regions of similarity between a nucleotide query sequence translated in all reading frames and a protein sequence database | |
| csblast (WSDL) | CS-BLAST finds regions of low similarity between peptides (Tuned Position-Specific Iterated BLAST) | |
| csblast_simple (WSDL) | CS-BLAST finds regions of low similarity between peptides (Tuned Position-Specific Iterated BLAST) | |
| megablast (WSDL) | megaBLAST finds regions of high similarity between a nucleotide query sequence and a nucleotide sequence database | |
| megablast_simple (WSDL) | megaBLAST finds regions of high similarity between a nucleotide query sequence and a nucleotide sequence database | |
| psiblast (WSDL) | psiBLAST finds regions of low similarity between peptides (Position-Specific Iterated BLAST) | |
| psiblast_simple (WSDL) | psiBLAST finds regions of low similarity between peptides (Position-Specific Iterated BLAST) | |
| tblastn (WSDL) | tBLASTn finds regions of similarity between a protein query sequence and a nucleotide sequence database dynamically translated in all reading frames | |
| tblastn_simple (WSDL) | tBLASTn finds regions of similarity between a protein query sequence and a nucleotide sequence database dynamically translated in all reading frames | |
| tblastx (WSDL) | tBLASTx finds regions of similarity between the six-frame translations of a nucleotide query sequence and the six-frame translations of a nucleotide sequence database | |
| tblastx_simple (WSDL) | tBLASTx finds regions of similarity between the six-frame translations of a nucleotide query sequence and the six-frame translations of a nucleotide sequence database | |
| Utils database creation | ||
| cathparse (WSDL) | Generates DCF file from raw CATH files. | |
| pdbtosp (WSDL) | Convert swissprot:PDB codes file to EMBL-like format. | |
| scopparse (WSDL) | Generate DCF file from raw SCOP files. | |
| ssematch (WSDL) | Search a DCF file for secondary structure matches. | |
| Utils misc | ||
| embossdata (WSDL) | Find and retrieve EMBOSS data files | |
| embossversion (WSDL) | Reports the current EMBOSS version number |
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