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Soaplab Web Services at Vital-IT

[Soaplab version: , build: Wed May 11 13:34:23 CEST 2016]

HELP

COLLAPSE
Category Service name Description
Alignment    
  extractalign (WSDL) Extract regions from a sequence alignment
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 display    
  boxshade (WSDL) BOXSHADE - Pretty Printing and Shading of MSA files
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) Display 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
  needle (WSDL) Needleman-Wunsch global alignment of two sequences
  needleall (WSDL) Many-to-many pairwise alignments of two sequence sets
  stretcher (WSDL) Needleman-Wunsch rapid global alignment of two sequences
Alignment local    
  domainrep (WSDL) Reorder DCF file to identify representative structures.
  matcher (WSDL) Waterman-Eggert local alignment of two sequences
  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) Find 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)
  eomega (WSDL) Multiple sequence alignment (ClustalO wrapper)
  eomegapp (WSDL) Profile with profile (ClustalO wrapper)
  eomegaps (WSDL) Single sequence with profile (ClustalO wrapper)
  eomegash (WSDL) Sequence with HMM (ClustalO wrapper)
  eomegasp (WSDL) Sequence with profile (ClustalO 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
Data resources    
  dbtell (WSDL) Display information about a public database
  servertell (WSDL) Display information about a public server
  showdb (WSDL) Display information on configured databases
  showserver (WSDL) Display information on configured servers
Data retrieval    
  codcopy (WSDL) Copy and reformat a codon usage table
  seqret (WSDL) Read and write (return) sequences
Data retrieval chemistry data    
  infobase (WSDL) Return information on a given nucleotide base
  inforesidue (WSDL) Return information on a given amino acid residue
Data retrieval feature data    
  featcopy (WSDL) Read and write a feature table
  featmerge (WSDL) Merge two overlapping feature tables
Data retrieval ontology data    
  edamdef (WSDL) Find EDAM ontology terms by definition
  edamhasinput (WSDL) Find EDAM ontology terms by has_input relation
  edamhasoutput (WSDL) Find EDAM ontology terms by has_output relation
  edamisformat (WSDL) Find EDAM ontology terms by is_format_of relation
  edamisid (WSDL) Find EDAM ontology terms by is_identifier_of relation
  edamname (WSDL) Find EDAM ontology terms by name
  godef (WSDL) Find GO ontology terms by definition
  goname (WSDL) Find GO ontology terms by name
  ontoget (WSDL) Get ontology term(s)
  ontogetcommon (WSDL) Get common ancestor for terms
  ontogetdown (WSDL) Get ontology term(s) by parent id
  ontogetobsolete (WSDL) Get ontology ontology terms
  ontogetroot (WSDL) Get ontology root terms by child identifier
  ontogetsibs (WSDL) Get ontology term(s) by id with common parent
  ontogetup (WSDL) Get ontology term(s) by id of child
  ontoisobsolete (WSDL) Report whether an ontology term id is obsolete
  ontotext (WSDL) Get ontology term(s) original full text
Data retrieval resource data    
  drfinddata (WSDL) Find public databases by data type
  drfindformat (WSDL) Find public databases by format
  drfindid (WSDL) Find public databases by identifier
  drfindresource (WSDL) Find public databases by resource
  drget (WSDL) Get data resource entries
  drtext (WSDL) Get data resource entries complete text
Data retrieval sequence data    
  coderet (WSDL) Extract CDS
  entret (WSDL) Retrieve sequence entries from flatfile databases and files
  extractalign (WSDL) Extract regions from a sequence alignment
  infoalign (WSDL) Display basic information about a multiple sequence alignment
  infoseq (WSDL) Display basic information about sequences
  seqxref (WSDL) Retrieve all database cross-references for a sequence entry
  seqxrefget (WSDL) Retrieve all cross-referenced data for a sequence entry
  showalign (WSDL) Display a multiple sequence alignment in pretty format
  whichdb (WSDL) Search all sequence databases for an entry and retrieve it
Data retrieval sequence data assembly data    
  infoassembly (WSDL) Display information about assemblies
Data retrieval text data    
  drtext (WSDL) Get data resource entries complete text
  entret (WSDL) Retrieve sequence entries from flatfile databases and files
  ontotext (WSDL) Get ontology term(s) original full text
  textget (WSDL) Get text data entries
  textsearch (WSDL) Search the textual description of sequence(s)
  xmltext (WSDL) Get XML document original full text
Data retrieval url data    
  urlget (WSDL) Get URLs of data resources
Data retrieval xml data    
  xmlget (WSDL) Get XML data
Database query    
  fetch (WSDL) Fetch get sequences
Display    
  cirdna (WSDL) Draw circular map of DNA constructs
  iep (WSDL) Calculate the isoelectric point of proteins
  lindna (WSDL) Draw linear maps of DNA constructs
  pepinfo (WSDL) Plot amino acid properties of a protein sequence in parallel.
  pepnet (WSDL) Draw a helical net for a protein sequence
  pepwheel (WSDL) Draw a helical wheel diagram for a protein sequence
  plotorf (WSDL) Plot potential open reading frames in a nucleotide 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
  showfeat (WSDL) Display features of a sequence in pretty format
  showpep (WSDL) Display protein sequences with features in pretty format
  sixpack (WSDL) Display a DNA sequence with 6-frame translation and ORFs
  topo (WSDL) Draw an image of a transmembrane protein
Documentation    
  seealso (WSDL) Find programs with similar function to a specified program
  tfm (WSDL) Display full documentation for an application
  wossdata (WSDL) Find programs by EDAM data
  wossinput (WSDL) Find programs by EDAM input data
  wossname (WSDL) Find programs by keywords in their short description
  wossoperation (WSDL) Find programs by EDAM operation
  wossoutput (WSDL) Find programs by EDAM output data
  wossparam (WSDL) Find programs by EDAM parameter
  wosstopic (WSDL) Find programs by EDAM topic
Edit    
  aligncopy (WSDL) Read and write alignments
  aligncopypair (WSDL) Read and write pairs from alignments
  biosed (WSDL) Replace or delete sequence sections
  codcopy (WSDL) Copy and reformat a codon usage table
  cutseq (WSDL) Remove a section from a sequence
  degapseq (WSDL) Remove non-alphabetic (e.g. gap) characters from sequences
  descseq (WSDL) Alter the name or description of a sequence.
  entret (WSDL) Retrieve 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) Read and write a feature table
  featmerge (WSDL) Merge two overlapping feature tables
  featreport (WSDL) Read and write a feature table
  feattext (WSDL) Return a feature table original text
  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) Mask all ambiguity characters in nucleotide sequences with N
  maskambigprot (WSDL) Mask 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 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) Read and write (return) 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
  seqcount (WSDL) Read and count sequences
  seqret (WSDL) Read and write (return) sequences
  seqretsetall (WSDL) Read and write (return) many sets of sequences
  sizeseq (WSDL) Sort sequences by size
  skipredundant (WSDL) Remove redundant sequences from an input set
  skipseq (WSDL) Read and write (return) 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) Remove vectors from the ends of nucleotide sequence(s)
  yank (WSDL) Add a sequence reference (a full USA) to a list file
Embnet    
  boxshade (WSDL) BOXSHADE - Pretty Printing and Shading of MSA files
  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
  fetch (WSDL) Fetch get sequences
  ipcr (WSDL) IPCR: Virtual PCR tool
  mafft (WSDL) MAFFT: Multiple alignment program for aa or nt sequences
  mafft_simple (WSDL) MAFFT: Multiple alignment program for aa or nt sequences
  readseq (WSDL) ReadSeq reads and reformats biosequences
  readseq_simple (WSDL) ReadSeq reads and reformats biosequences
  tmpred (WSDL) Prediction of Transmembrane Regions and Orientation
Enzyme kinetics    
  findkm (WSDL) Calculate and plot enzyme reaction data
Feature tables    
  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) Find neighbouring pairs of features in sequence(s)
Nucleic 2d structure    
  banana (WSDL) Plot bending and curvature data for B-DNA
  btwisted (WSDL) Calculate the twisting in a B-DNA sequence
  einverted (WSDL) Find inverted repeats in nucleotide sequences
  ovrnaalifold (WSDL) Calculate secondary structures for a set of aligned RNAs
  ovrnaalifoldpf (WSDL) Calculate secondary structures for a set of aligned RNAs (partition)
  ovrnacofold (WSDL) Calculate secondary structures of RNA dimers
  ovrnacofoldconc (WSDL) Calculate secondary structures of RNA dimers (concentrations)
  ovrnacofoldpf (WSDL) Calculate secondary structures of RNA dimers (partitioning)
  ovrnadistance (WSDL) Calculate distances between RNA secondary structures
  ovrnaduplex (WSDL) Predict RNA duplex (hybridization) sites and structure
  ovrnaeval (WSDL) Calculate energy of RNA sequences with a given secondary structure
  ovrnaevalpair (WSDL) Calculate energy of RNA sequences on given secondary structure
  ovrnafold (WSDL) Calculate min. energy RNA structure / pair probabilities (partition)
  ovrnafoldpf (WSDL) Calculate min. energy RNA structure / pair probabilities
  ovrnaheat (WSDL) Calculate specific heat of RNA melting
  ovrnainverse (WSDL) Find RNA sequences with a given secondary structure
  ovrnalfold (WSDL) Calculate locally stable secondary structures of RNAs
  ovrnaplot (WSDL) Draw RNA secondary structures
  ovrnasubopt (WSDL) Calculate suboptimal secondary structure of RNA
  sirna (WSDL) Find siRNA duplexes in mRNA
Nucleic codon usage    
  cai (WSDL) Calculate codon adaptation index
  chips (WSDL) Calculate Nc codon usage statistic
  codcmp (WSDL) Codon usage table comparison
  codcopy (WSDL) Copy and reformat a codon usage table
  cusp (WSDL) Create a codon usage table from nucleotide sequence(s)
  syco (WSDL) Draw synonymous codon usage statistic 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) Calculate nucleic acid melting temperature
  density (WSDL) Draw a nucleic acid density plot
  freak (WSDL) Generate residue/base frequency table or plot
  isochore (WSDL) Plot isochores in DNA sequences
  wordcount (WSDL) Count and extract unique words in molecular 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 functional sites    
  marscan (WSDL) Find matrix/scaffold recognition (MRS) signatures in DNA sequences
  sirna (WSDL) Find siRNA duplexes in mRNA
  trimest (WSDL) Remove poly-A tails from nucleotide sequences
Nucleic gene finding    
  checktrans (WSDL) Report STOP codons and ORF statistics of a protein
  getorf (WSDL) Find and extract open reading frames (ORFs)
  marscan (WSDL) Find 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 statistic 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)
Nucleic mutation    
  msbar (WSDL) Mutate a sequence
  shuffleseq (WSDL) Shuffle a set of sequences maintaining composition
Nucleic primers    
  eprimer3 (WSDL) Pick 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 properties    
  banana (WSDL) Plot bending and curvature data for B-DNA
  btwisted (WSDL) Calculate the twisting in a B-DNA sequence
  dan (WSDL) Calculate nucleic acid melting temperature
Nucleic repeats    
  einverted (WSDL) Find inverted repeats in nucleotide sequences
  equicktandem (WSDL) Find tandem repeats in nucleotide sequences
  etandem (WSDL) Find tandem repeats in a nucleotide sequence
  palindrome (WSDL) Find 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) Display sequences with features in pretty format
  silent (WSDL) Find restriction sites to insert (mutate) with no translation change
Nucleic rna folding    
  ovrnaalifold (WSDL) Calculate secondary structures for a set of aligned RNAs
  ovrnaalifoldpf (WSDL) Calculate secondary structures for a set of aligned RNAs (partition)
  ovrnacofold (WSDL) Calculate secondary structures of RNA dimers
  ovrnacofoldconc (WSDL) Calculate secondary structures of RNA dimers (concentrations)
  ovrnacofoldpf (WSDL) Calculate secondary structures of RNA dimers (partitioning)
  ovrnadistance (WSDL) Calculate distances between RNA secondary structures
  ovrnaduplex (WSDL) Predict RNA duplex (hybridization) sites and structure
  ovrnaeval (WSDL) Calculate energy of RNA sequences with a given secondary structure
  ovrnaevalpair (WSDL) Calculate energy of RNA sequences on given secondary structure
  ovrnafold (WSDL) Calculate min. energy RNA structure / pair probabilities (partition)
  ovrnafoldpf (WSDL) Calculate min. energy RNA structure / pair probabilities
  ovrnaheat (WSDL) Calculate specific heat of RNA melting
  ovrnainverse (WSDL) Find RNA sequences with a given secondary structure
  ovrnalfold (WSDL) Calculate locally stable secondary structures of RNAs
  ovrnaplot (WSDL) Draw RNA secondary structures
  ovrnasubopt (WSDL) Calculate suboptimal secondary structure of RNA
Nucleic transcription    
  marscan (WSDL) Find matrix/scaffold recognition (MRS) signatures in DNA sequences
  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
  checktrans (WSDL) Report STOP codons and ORF statistics of a protein
  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) Display sequences with features in pretty format
  sixpack (WSDL) Display a DNA sequence with 6-frame translation and ORFs
  transeq (WSDL) Translate nucleic acid sequences
Ontology    
  ontocount (WSDL) Count ontology term(s)
  ontoget (WSDL) Get ontology term(s)
  ontogetcommon (WSDL) Get common ancestor for terms
  ontogetdown (WSDL) Get ontology term(s) by parent id
  ontogetobsolete (WSDL) Get ontology ontology terms
  ontogetroot (WSDL) Get ontology root terms by child identifier
  ontogetsibs (WSDL) Get ontology term(s) by id with common parent
  ontogetup (WSDL) Get ontology term(s) by id of child
  ontoisobsolete (WSDL) Report whether an ontology term id is obsolete
  ontotext (WSDL) Get ontology term(s) original full text
Ontology edam    
  drfinddata (WSDL) Find public databases by data type
  drfindformat (WSDL) Find public databases by format
  drfindid (WSDL) Find public databases by identifier
  drfindresource (WSDL) Find public databases by resource
  edamdef (WSDL) Find EDAM ontology terms by definition
  edamhasinput (WSDL) Find EDAM ontology terms by has_input relation
  edamhasoutput (WSDL) Find EDAM ontology terms by has_output relation
  edamisformat (WSDL) Find EDAM ontology terms by is_format_of relation
  edamisid (WSDL) Find EDAM ontology terms by is_identifier_of relation
  edamname (WSDL) Find EDAM ontology terms by name
  wossdata (WSDL) Find programs by EDAM data
  wossinput (WSDL) Find programs by EDAM input data
  wossoperation (WSDL) Find programs by EDAM operation
  wossoutput (WSDL) Find programs by EDAM output data
  wossparam (WSDL) Find programs by EDAM parameter
  wosstopic (WSDL) Find programs by EDAM topic
Ontology go    
  godef (WSDL) Find GO ontology terms by definition
  goname (WSDL) Find GO ontology terms by name
Ontology taxonomy    
  taxget (WSDL) Get taxon(s)
  taxgetdown (WSDL) Get descendants of taxon(s)
  taxgetrank (WSDL) Get parents of taxon(s)
  taxgetspecies (WSDL) Get all species under taxon(s)
  taxgetup (WSDL) Get parents of taxon(s)
Phylogeny consensus    
  fconsense (WSDL) Majority-rule and strict consensus tree
  ftreedist (WSDL) Calculate distances between trees
  ftreedistpair (WSDL) Calculate distance 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) Estimate 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) Calculate 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) Predict protein secondary structure using GOR method
  helixturnhelix (WSDL) Identify nucleic acid-binding motifs in protein sequences
  pepcoil (WSDL) Predict 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
  tmpred (WSDL) Prediction of Transmembrane Regions and Orientation
Protein 3d structure    
  domainrep (WSDL) Reorder DCF file to identify representative structures.
  psiphi (WSDL) Calculates phi and psi torsion angles from protein coordinates
Protein composition    
  backtranambig (WSDL) Back-translate a protein sequence to ambiguous nucleotide sequence
  backtranseq (WSDL) Back-translate a protein sequence to a nucleotide sequence
  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
  mwfilter (WSDL) Filter noisy data from molecular weights file
  oddcomp (WSDL) Identify proteins with specified sequence word composition
  pepdigest (WSDL) Report on protein proteolytic enzyme or reagent cleavage sites
  pepinfo (WSDL) Plot amino acid properties of a protein sequence in parallel.
  pepstats (WSDL) Calculate statistics of protein properties
  wordcount (WSDL) Count and extract unique words in molecular sequence(s)
Protein domains    
  cathparse (WSDL) Generate DCF file from raw CATH files.
  domainrep (WSDL) Reorder DCF file to identify representative structures.
  helixturnhelix (WSDL) Identify nucleic acid-binding motifs in protein sequences
  pepcoil (WSDL) Predict coiled coil regions in protein sequences
  rocon (WSDL) Generate a hits file from comparing two DHF files
  scopparse (WSDL) Generate DCF file from raw SCOP files.
  seqwords (WSDL) Generate DHF files from keyword search of UniProt.
  ssematch (WSDL) Search a DCF file for secondary structure matches.
Protein functional sites    
  sigcleave (WSDL) Report on signal cleavage sites in a protein sequence
  sigscan (WSDL) Generate hits (DHF file) from a signature search
  tmap (WSDL) Predict and plot transmembrane segments in protein sequences
  topo (WSDL) Draw an image of a transmembrane protein
Protein motifs    
  antigenic (WSDL) Find antigenic sites in proteins
  digest (WSDL) Report on protein proteolytic enzyme or reagent cleavage sites
  ememetext (WSDL) Multiple EM for Motif Elicitation. Text file only.
  epestfind (WSDL) Find PEST motifs as potential proteolytic cleavage sites
  fuzzpro (WSDL) Search for patterns in protein sequences
  fuzztran (WSDL) Search for patterns in protein sequences (translated)
  patmatdb (WSDL) Search protein sequences with a sequence motif
  patmatmotifs (WSDL) Scan a protein sequence with motifs from the PROSITE database
  preg (WSDL) Regular expression search of protein sequence(s)
  pscan (WSDL) Scan protein sequence(s) with fingerprints from the PRINTS database
  sigcleave (WSDL) Report on signal cleavage sites in a protein sequence
Protein mutation    
  msbar (WSDL) Mutate a sequence
  shuffleseq (WSDL) Shuffle 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
  sigscan (WSDL) Generate hits (DHF file) from a signature search
Protein properties    
  charge (WSDL) Draw a protein charge plot
  hmoment (WSDL) Calculate and plot hydrophobic moment for protein sequence(s)
  iep (WSDL) Calculate the isoelectric point of proteins
  octanol (WSDL) Draw a White-Wimley protein hydropathy plot
  pepinfo (WSDL) Plot amino acid properties of a protein sequence in parallel.
  pepstats (WSDL) Calculate 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
Utils    
  embossdata (WSDL) Find and retrieve EMBOSS data files
  embossversion (WSDL) Report the current EMBOSS version number
Utils database creation    
  cathparse (WSDL) Generate 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.


Soaplab2 documentation
Contact:
Spinet Web Client to Soaplab2 services
Click on this Help button to get detailed information how to use it and what to avoid.

And, by the way, this is a spinet:

What is a spinet

Tooltips library from TwinHelix Designs
Inject example input data
Clicking on this button fills many of the services above by a testing input data. You can then run them without bothering to find how to feed them.

Sorry, not yet implemented...

Collapse/close all open panels
All currently open service panels will be closed - and your screen will be again manageable.

However, all contents of the panel input forms will be kept. When you click again on any previously open service name, you will see what you left there.