Hobit @ DKFZ - Webservices in Bioinformatics

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Webservices in Bioinformatics - Hobit @ DKFZ

Contributing to the HOBIT (Helmholtz Open Bioinformatics Technology) project, the HUSAR Bioinformatics Lab provides a number of its applications and developments using web service and HOBIT standards.

The HOBIT projects aims to improve the mutual interconnectivity of its peers by providing documentation, guidelines, tutorials, recommendations for services and additional schemas for bioinformatics applications.

DKFZ bioinformatics web-services powered by Soaplab
SoapDB - Soap access to sequence databases at DKFZ
SoapGO - Soap access to GO (Gene Ontology) related methods

The HUSAR Bioinformatics Lab at DKFZ provides a number of applications through web-service technology employing a SoapLab server:

Examples:
The usage of these webservices can be studied in some example clients for Perl, Java and C#.

Alignment consensus

Program name	Web service	Description
cons	WSDL	Creates a consensus from multiple alignments
megamerger	WSDL	Merge two large overlapping nucleic acid sequences
merger	WSDL	Merge two overlapping nucleic acid sequences

Alignment differences

Program name	Web service	Description
diffseq	WSDL	Find differences between nearly identical sequences

Alignment dot plots

Program name	Web service	Description
dotmatcher	WSDL	Displays a thresholded dotplot of two sequences
dotpath	WSDL	Displays a non-overlapping wordmatch dotplot of two sequences
dottup	WSDL	Displays a wordmatch dotplot of two sequences
polydot	WSDL	Displays all-against-all dotplots of a set of sequences

Alignment global

Program name	Web service	Description
est2genome	WSDL	Align EST and genomic DNA sequences
needle	WSDL	Needleman-Wunsch global alignment
stretcher	WSDL	Finds the best global alignment between two sequences

Alignment local

Program name	Web service	Description
matcher	WSDL	Finds the best local alignments between two sequences
seqmatchall	WSDL	Does an all-against-all comparison of a set of sequences
supermatcher	WSDL	Finds a match of a large sequence against one or more sequences
water	WSDL	Smith-Waterman local alignment
wordmatch	WSDL	Finds all exact matches of a given size between 2 sequences

Alignment multiple

Program name	Web service	Description
emma	WSDL	Multiple alignment program - interface to ClustalW program
infoalign	WSDL	Information on a multiple sequence alignment
plotcon	WSDL	Plots the quality of conservation of a sequence alignment
prettyplot	WSDL	Displays aligned sequences, with colouring and boxing
showalign	WSDL	Displays a multiple sequence alignment
tranalign	WSDL	Align nucleic coding regions given the aligned proteins

Display

Program name	Web service	Description
abiview	WSDL	Reads ABI file and display the trace
cirdna	WSDL	Draws circular maps of DNA constructs
lindna	WSDL	Draws linear maps of DNA constructs
pepnet	WSDL	Displays proteins as a helical net
pepwheel	WSDL	Shows protein sequences as helices
prettyplot	WSDL	Displays aligned sequences, with colouring and boxing
prettyseq	WSDL	Output sequence with translated ranges
remap	WSDL	Display a sequence with restriction cut sites, translation etc
seealso	WSDL	Finds programs sharing group names
showalign	WSDL	Displays a multiple sequence alignment
showdb	WSDL	Displays information on the currently available databases
showfeat	WSDL	Show features of a sequence
showseq	WSDL	Display a sequence with features, translation etc
sixpack	WSDL	Display a DNA sequence with 6-frame translation and ORFs
textsearch	WSDL	Search sequence documentation text. SRS and Entrez are faster!

Edit

Program name	Web service	Description
biosed	WSDL	Replace or delete sequence sections
cutseq	WSDL	Removes a specified section from a sequence
degapseq	WSDL	Removes gap characters from sequences
descseq	WSDL	Alter the name or description of a sequence
entret	WSDL	Reads and writes (returns) flatfile entries
extractfeat	WSDL	Extract features from a sequence
extractseq	WSDL	Extract regions from a sequence
listor	WSDL	Writes a list file of the logical OR of two sets of sequences
maskfeat	WSDL	Mask off features of a sequence
maskseq	WSDL	Mask off regions of a sequence
newseq	WSDL	Type in a short new sequence
noreturn	WSDL	Removes carriage return from ASCII files
notseq	WSDL	Excludes a set of sequences and writes out the remaining ones
nthseq	WSDL	Writes one sequence from a multiple set of sequences
pasteseq	WSDL	Insert one sequence into another
revseq	WSDL	Reverse and complement a sequence
seqret	WSDL	Reads and writes (returns) sequences
seqretsplit	WSDL	Reads and writes (returns) sequences in individual files
skipseq	WSDL	Reads and writes (returns) sequences, skipping the first few
splitter	WSDL	Split a sequence into (overlapping) smaller sequences
trimest	WSDL	Trim poly-A tails off EST sequences
trimseq	WSDL	Trim ambiguous bits off the ends of sequences
union	WSDL	Reads sequence fragments and builds one sequence
vectorstrip	WSDL	Strips out DNA between a pair of vector sequences
yank	WSDL	Reads a sequence range, appends the full USA to a list file

Enzyme kinetics

Program name	Web service	Description
findkm	WSDL	Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot

Feature tables

Program name	Web service	Description
coderet	WSDL	Extract CDS, mRNA and translations from feature tables
extractfeat	WSDL	Extract features from a sequence
maskfeat	WSDL	Mask off features of a sequence
showfeat	WSDL	Show features of a sequence
twofeat	WSDL	Finds neighbouring pairs of features in sequences

Information

Program name	Web service	Description
infoalign	WSDL	Information on a multiple sequence alignment
infoseq	WSDL	Displays some simple information about sequences
seealso	WSDL	Finds programs sharing group names
showdb	WSDL	Displays information on the currently available databases
textsearch	WSDL	Search sequence documentation text. SRS and Entrez are faster!
tfm	WSDL	Displays a program's help documentation manual
whichdb	WSDL	Search all databases for an entry
wossname	WSDL	Finds programs by keywords in their one-line documentation

Nucleic 2d structure

Program name	Web service	Description
einverted	WSDL	Finds DNA inverted repeats

Nucleic codon usage

Program name	Web service	Description
cai	WSDL	CAI codon adaptation index
chips	WSDL	Codon usage statistics
codcmp	WSDL	Codon usage table comparison
cusp	WSDL	Create a codon usage table
syco	WSDL	Synonymous codon usage Gribskov statistic plot

Nucleic composition

Program name	Web service	Description
banana	WSDL	Bending and curvature plot in B-DNA
btwisted	WSDL	Calculates the twisting in a B-DNA sequence
chaos	WSDL	Create a chaos game representation plot for a sequence
compseq	WSDL	Counts the composition of dimer/trimer/etc words in a sequence
dan	WSDL	Calculates DNA RNA/DNA melting temperature
freak	WSDL	Residue/base frequency table or plot
isochore	WSDL	Plots isochores in large DNA sequences
sirna	WSDL	Finds siRNA duplexes in mRNA
wordcount	WSDL	Counts words of a specified size in a DNA sequence

Nucleic cpg islands

Program name	Web service	Description
cpgplot	WSDL	Plot CpG rich areas
cpgreport	WSDL	Reports all CpG rich regions
geecee	WSDL	Calculates the fractional GC content of nucleic acid sequences
newcpgreport	WSDL	Report CpG rich areas
newcpgseek	WSDL	Reports CpG rich regions

Nucleic gene finding

Program name	Web service	Description
getorf	WSDL	Finds and extracts open reading frames (ORFs)
marscan	WSDL	Finds MAR/SAR sites in nucleic sequences
plotorf	WSDL	Plot potential open reading frames
showorf	WSDL	Pretty output of DNA translations
sixpack	WSDL	Display a DNA sequence with 6-frame translation and ORFs
syco	WSDL	Synonymous codon usage Gribskov statistic plot
tcode	WSDL	Fickett TESTCODE statistic to identify protein-coding DNA
wobble	WSDL	Wobble base plot

Nucleic motifs

Program name	Web service	Description
dreg	WSDL	Regular expression search of a nucleotide sequence
fuzznuc	WSDL	Nucleic acid pattern search
fuzztran	WSDL	Protein pattern search after translation
marscan	WSDL	Finds MAR/SAR sites in nucleic sequences

Nucleic mutation

Program name	Web service	Description
msbar	WSDL	Mutate sequence beyond all recognition
shuffleseq	WSDL	Shuffles a set of sequences maintaining composition

Nucleic primers

Program name	Web service	Description
eprimer3	WSDL	Picks PCR primers and hybridization oligos
primersearch	WSDL	Searches DNA sequences for matches with primer pairs
stssearch	WSDL	Searches a DNA database for matches with a set of STS primers

Nucleic profiles

Program name	Web service	Description
profit	WSDL	Scan a sequence or database with a matrix or profile
prophecy	WSDL	Creates matrices/profiles from multiple alignments
prophet	WSDL	Gapped alignment for profiles

Nucleic repeats

Program name	Web service	Description
einverted	WSDL	Finds DNA inverted repeats
equicktandem	WSDL	Finds tandem repeats
etandem	WSDL	Looks for tandem repeats in a nucleotide sequence
palindrome	WSDL	Looks for inverted repeats in a nucleotide sequence

Nucleic restriction

Program name	Web service	Description
recoder	WSDL	Remove restriction sites but maintain the same translation
redata	WSDL	Search REBASE for enzyme name, references, suppliers etc
remap	WSDL	Display a sequence with restriction cut sites, translation etc
restover	WSDL	Finds restriction enzymes that produce a specific overhang
restrict	WSDL	Finds restriction enzyme cleavage sites
showseq	WSDL	Display a sequence with features, translation etc
silent	WSDL	Silent mutation restriction enzyme scan

Nucleic transcription

Program name	Web service	Description
tfscan	WSDL	Scans DNA sequences for transcription factors

Nucleic translation

Program name	Web service	Description
backtranseq	WSDL	Back translate a protein sequence
coderet	WSDL	Extract CDS, mRNA and translations from feature tables
plotorf	WSDL	Plot potential open reading frames
prettyseq	WSDL	Output sequence with translated ranges
remap	WSDL	Display a sequence with restriction cut sites, translation etc
showorf	WSDL	Pretty output of DNA translations
showseq	WSDL	Display a sequence with features, translation etc
sixpack	WSDL	Display a DNA sequence with 6-frame translation and ORFs
transeq	WSDL	Translate nucleic acid sequences

Phylogeny distance matrix

Program name	Web service	Description
distmat	WSDL	Creates a distance matrix from multiple alignments

Protein 2d structure

Program name	Web service	Description
garnier	WSDL	Predicts protein secondary structure
helixturnhelix	WSDL	Report nucleic acid binding motifs
hmoment	WSDL	Hydrophobic moment calculation
pepcoil	WSDL	Predicts coiled coil regions
pepnet	WSDL	Displays proteins as a helical net
pepwheel	WSDL	Shows protein sequences as helices
tmap	WSDL	Displays membrane spanning regions

Protein 3d structure

Program name	Web service	Description
psiphi	WSDL	Calculates phi and psi torsion angles from cleaned EMBOSS-style protein co-ordinate file

Protein composition

Program name	Web service	Description
backtranseq	WSDL	Back translate a protein sequence
charge	WSDL	Protein charge plot
checktrans	WSDL	Reports STOP codons and ORF statistics of a protein
compseq	WSDL	Counts the composition of dimer/trimer/etc words in a sequence
emowse	WSDL	Protein identification by mass spectrometry
freak	WSDL	Residue/base frequency table or plot
iep	WSDL	Calculates the isoelectric point of a protein
mwcontam	WSDL	Shows molwts that match across a set of files
mwfilter	WSDL	Filter noisy molwts from mass spec output
octanol	WSDL	Displays protein hydropathy
pepinfo	WSDL	Plots simple amino acid properties in parallel
pepstats	WSDL	Protein statistics
pepwindow	WSDL	Displays protein hydropathy
pepwindowall	WSDL	Displays protein hydropathy of a set of sequences

Protein motifs

Program name	Web service	Description
antigenic	WSDL	Finds antigenic sites in proteins
digest	WSDL	Protein proteolytic enzyme or reagent cleavage digest
epestfind	WSDL	Finds PEST motifs as potential proteolytic cleavage sites
fuzzpro	WSDL	Protein pattern search
fuzztran	WSDL	Protein pattern search after translation
helixturnhelix	WSDL	Report nucleic acid binding motifs
oddcomp	WSDL	Finds protein sequence regions with a biased composition
patmatdb	WSDL	Search a protein sequence with a motif
patmatmotifs	WSDL	Search a PROSITE motif database with a protein sequence
pepcoil	WSDL	Predicts coiled coil regions
preg	WSDL	Regular expression search of a protein sequence
pscan	WSDL	Scans proteins using PRINTS
sigcleave	WSDL	Reports protein signal cleavage sites

Protein mutation

Program name	Web service	Description
msbar	WSDL	Mutate sequence beyond all recognition
shuffleseq	WSDL	Shuffles a set of sequences maintaining composition

Protein profiles

Program name	Web service	Description
profit	WSDL	Scan a sequence or database with a matrix or profile
prophecy	WSDL	Creates matrices/profiles from multiple alignments
prophet	WSDL	Gapped alignment for profiles

Utils misc

Program name	Web service	Description
embossversion	WSDL	Writes the current EMBOSS version number

W3htask

Program name	Web service	Description
domainsweep	WSDL	Identifies the domain architecture within a protein sequence
protsweep	WSDL	A Protein Identification Tool
twodsweep	WSDL

method 2.1: seqret1() - retrieve single sequence entry from databases

<message name="seqret1Request">
 <part name="usa" type="xsd:string"/>
 <part name="format" type="xsd:string"/>
</message>

<message name="seqret1Response">
 <part name="outseq" type="xsd:string"/>
</message>

Example Request

Example Response

method 2.2: srsEntry() - retrieve entries from SRS datbase system: databases

<message name="srsEntryRequest">
 <part name="query" type="xsd:string"/>
</message>

<message name="srsEntryResponse">
 <part name="entry" type="xsd:string"/>
</message>

Example Request

Example Response

method 2.3: srsEntryFields() - retrieve entries from SRS datbase system with fields filter: databases

<message name="srsEntryFieldsRequest">
 <part name="query" type="xsd:string"/>
 <part name="fields" type="xsd:string"/>
</message>

<message name="srsEntryFieldsResponse">
 <part name="entry" type="xsd:string"/>
</message>

Example Request

method 2.4: srsEntryView() - retrieve entries from SRS datbase system in a given View: databases

<message name="srsEntryViewRequest">
 <part name="query" type="xsd:string"/>
 <part name="view" type="xsd:string"/>
</message>

<message name="srsEntryViewResponse">
 <part name="entry" type="xsd:string"/>
</message>

Example Request

method 2.5: srsEntryXml() - retrieve entries from SRS datbase system in XML format: databases

<message name="srsEntryXmlRequest">
 <part name="query" type="xsd:string"/>
 
</message>

<message name="srsEntryXmlResponse">
 <part name="srs-result"  type="xsd:anyType"/>
</message>

Example Request

Example Response

The following represents work-in-progress and is likely to change:

method 3.1: go-ancestors() - retrieve GO ancestor nodes

<message name="go-ancestorsRequest">
 <part name="acc-sequence" element="hobit_DKFZ:acc-sequence"/>
</message>

<message name="go-ancestorsResponse">
 <part name="go-pairs" element="hobit_DKFZ:go-pairs"/>
</message>


<schema targetNamespace="urn:hobit-dkfz-soapgo"
 xmlns:hobit-DKFZ="urn:hobit-dkfz-soapgo">

 <!-- .... -->

 <element name="acc-sequence" type="hobit-DKFZ:Go-acc-array"/>
 <element name="go-pairs" type="hobit-DKFZ:Go-pair-ancestors-array"/>
</schema>

Data organisation

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