HUSAR Bioinformatics Lab
Deutsches Krebsforschungszentrum Genomics Proteomics Core Facility
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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.

Content:
  1. DKFZ bioinformatics web-services powered by Soaplab
  2. SoapDB - Soap access to sequence databases at DKFZ
  3. SoapGO - Soap access to GO (Gene Ontology) related methods


 
1. DKFZ bioinformatics web-services powered by Soaplab:
 
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 nameWeb serviceDescription
consCreates a consensus from multiple alignments
megamergerMerge two large overlapping nucleic acid sequences
mergerMerge two overlapping nucleic acid sequences

Alignment differences

Program nameWeb serviceDescription
diffseqFind differences between nearly identical sequences

Alignment dot plots

Program nameWeb serviceDescription
dotmatcherDisplays a thresholded dotplot of two sequences
dotpathDisplays a non-overlapping wordmatch dotplot of two sequences
dottupDisplays a wordmatch dotplot of two sequences
polydotDisplays all-against-all dotplots of a set of sequences

Alignment global

Program nameWeb serviceDescription
est2genomeAlign EST and genomic DNA sequences
needleNeedleman-Wunsch global alignment
stretcherFinds the best global alignment between two sequences

Alignment local

Program nameWeb serviceDescription
matcherFinds the best local alignments between two sequences
seqmatchallDoes an all-against-all comparison of a set of sequences
supermatcherFinds a match of a large sequence against one or more sequences
waterSmith-Waterman local alignment
wordmatchFinds all exact matches of a given size between 2 sequences

Alignment multiple

Program nameWeb serviceDescription
emmaMultiple alignment program - interface to ClustalW program
infoalignInformation on a multiple sequence alignment
plotconPlots the quality of conservation of a sequence alignment
prettyplotDisplays aligned sequences, with colouring and boxing
showalignDisplays a multiple sequence alignment
tranalignAlign nucleic coding regions given the aligned proteins

Display

Program nameWeb serviceDescription
abiviewReads ABI file and display the trace
cirdnaDraws circular maps of DNA constructs
lindnaDraws linear maps of DNA constructs
pepnetDisplays proteins as a helical net
pepwheelShows protein sequences as helices
prettyplotDisplays aligned sequences, with colouring and boxing
prettyseqOutput sequence with translated ranges
remapDisplay a sequence with restriction cut sites, translation etc
seealsoFinds programs sharing group names
showalignDisplays a multiple sequence alignment
showdbDisplays information on the currently available databases
showfeatShow features of a sequence
showseqDisplay a sequence with features, translation etc
sixpackDisplay a DNA sequence with 6-frame translation and ORFs
textsearchSearch sequence documentation text. SRS and Entrez are faster!

Edit

Program nameWeb serviceDescription
biosedReplace or delete sequence sections
cutseqRemoves a specified section from a sequence
degapseqRemoves gap characters from sequences
descseqAlter the name or description of a sequence
entretReads and writes (returns) flatfile entries
extractfeatExtract features from a sequence
extractseqExtract regions from a sequence
listorWrites a list file of the logical OR of two sets of sequences
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
notseqExcludes a set of sequences and writes out the remaining ones
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
seqretReads and writes (returns) sequences
seqretsplitReads and writes (returns) sequences in individual files
skipseqReads and writes (returns) sequences, skipping the first few
splitterSplit a sequence into (overlapping) smaller sequences
trimestTrim poly-A tails off EST sequences
trimseqTrim ambiguous bits off the ends of sequences
unionReads sequence fragments and builds one sequence
vectorstripStrips out DNA between a pair of vector sequences
yankReads a sequence range, appends the full USA to a list file

Enzyme kinetics

Program nameWeb serviceDescription
findkmFind Km and Vmax for an enzyme reaction by a Hanes/Woolf plot

Feature tables

Program nameWeb serviceDescription
coderetExtract CDS, mRNA and translations from feature tables
extractfeatExtract features from a sequence
maskfeatMask off features of a sequence
showfeatShow features of a sequence
twofeatFinds neighbouring pairs of features in sequences

Information

Program nameWeb serviceDescription
infoalignInformation on a multiple sequence alignment
infoseqDisplays some simple information about sequences
seealsoFinds programs sharing group names
showdbDisplays information on the currently available databases
textsearchSearch sequence documentation text. SRS and Entrez are faster!
tfmDisplays a program's help documentation manual
whichdbSearch all databases for an entry
wossnameFinds programs by keywords in their one-line documentation

Nucleic 2d structure

Program nameWeb serviceDescription
einvertedFinds DNA inverted repeats

Nucleic codon usage

Program nameWeb serviceDescription
caiCAI codon adaptation index
chipsCodon usage statistics
codcmpCodon usage table comparison
cuspCreate a codon usage table
sycoSynonymous codon usage Gribskov statistic plot

Nucleic composition

Program nameWeb serviceDescription
bananaBending and curvature plot in B-DNA
btwistedCalculates the twisting in a B-DNA sequence
chaosCreate a chaos game representation plot for a sequence
compseqCounts the composition of dimer/trimer/etc words in a sequence
danCalculates DNA RNA/DNA melting temperature
freakResidue/base frequency table or plot
isochorePlots isochores in large DNA sequences
sirnaFinds siRNA duplexes in mRNA
wordcountCounts words of a specified size in a DNA sequence

Nucleic cpg islands

Program nameWeb serviceDescription
cpgplotPlot CpG rich areas
cpgreportReports all CpG rich regions
geeceeCalculates the fractional GC content of nucleic acid sequences
newcpgreportReport CpG rich areas
newcpgseekReports CpG rich regions

Nucleic gene finding

Program nameWeb serviceDescription
getorfFinds and extracts open reading frames (ORFs)
marscanFinds MAR/SAR sites in nucleic sequences
plotorfPlot potential open reading frames
showorfPretty output of DNA translations
sixpackDisplay a DNA sequence with 6-frame translation and ORFs
sycoSynonymous codon usage Gribskov statistic plot
tcodeFickett TESTCODE statistic to identify protein-coding DNA
wobbleWobble base plot

Nucleic motifs

Program nameWeb serviceDescription
dregRegular expression search of a nucleotide sequence
fuzznucNucleic acid pattern search
fuzztranProtein pattern search after translation
marscanFinds MAR/SAR sites in nucleic sequences

Nucleic mutation

Program nameWeb serviceDescription
msbarMutate sequence beyond all recognition
shuffleseqShuffles a set of sequences maintaining composition

Nucleic primers

Program nameWeb serviceDescription
eprimer3Picks PCR primers and hybridization oligos
primersearchSearches DNA sequences for matches with primer pairs
stssearchSearches a DNA database for matches with a set of STS primers

Nucleic profiles

Program nameWeb serviceDescription
profitScan a sequence or database with a matrix or profile
prophecyCreates matrices/profiles from multiple alignments
prophetGapped alignment for profiles

Nucleic repeats

Program nameWeb serviceDescription
einvertedFinds DNA inverted repeats
equicktandemFinds tandem repeats
etandemLooks for tandem repeats in a nucleotide sequence
palindromeLooks for inverted repeats in a nucleotide sequence

Nucleic restriction

Program nameWeb serviceDescription
recoderRemove restriction sites but maintain the same translation
redataSearch REBASE for enzyme name, references, suppliers etc
remapDisplay a sequence with restriction cut sites, translation etc
restoverFinds restriction enzymes that produce a specific overhang
restrictFinds restriction enzyme cleavage sites
showseqDisplay a sequence with features, translation etc
silentSilent mutation restriction enzyme scan

Nucleic transcription

Program nameWeb serviceDescription
tfscanScans DNA sequences for transcription factors

Nucleic translation

Program nameWeb serviceDescription
backtranseqBack translate a protein sequence
coderetExtract CDS, mRNA and translations from feature tables
plotorfPlot potential open reading frames
prettyseqOutput sequence with translated ranges
remapDisplay a sequence with restriction cut sites, translation etc
showorfPretty output of DNA translations
showseqDisplay a sequence with features, translation etc
sixpackDisplay a DNA sequence with 6-frame translation and ORFs
transeqTranslate nucleic acid sequences

Phylogeny distance matrix

Program nameWeb serviceDescription
distmatCreates a distance matrix from multiple alignments

Protein 2d structure

Program nameWeb serviceDescription
garnierPredicts protein secondary structure
helixturnhelixReport nucleic acid binding motifs
hmomentHydrophobic moment calculation
pepcoilPredicts coiled coil regions
pepnetDisplays proteins as a helical net
pepwheelShows protein sequences as helices
tmapDisplays membrane spanning regions

Protein 3d structure

Program nameWeb serviceDescription
psiphiCalculates phi and psi torsion angles from cleaned EMBOSS-style protein co-ordinate file

Protein composition

Program nameWeb serviceDescription
backtranseqBack translate a protein sequence
chargeProtein charge plot
checktransReports STOP codons and ORF statistics of a protein
compseqCounts the composition of dimer/trimer/etc words in a sequence
emowseProtein identification by mass spectrometry
freakResidue/base frequency table or plot
iepCalculates the isoelectric point of a protein
mwcontamShows molwts that match across a set of files
mwfilterFilter noisy molwts from mass spec output
octanolDisplays protein hydropathy
pepinfoPlots simple amino acid properties in parallel
pepstatsProtein statistics
pepwindowDisplays protein hydropathy
pepwindowallDisplays protein hydropathy of a set of sequences

Protein motifs

Program nameWeb serviceDescription
antigenicFinds antigenic sites in proteins
digestProtein proteolytic enzyme or reagent cleavage digest
epestfindFinds PEST motifs as potential proteolytic cleavage sites
fuzzproProtein pattern search
fuzztranProtein pattern search after translation
helixturnhelixReport nucleic acid binding motifs
oddcompFinds protein sequence regions with a biased composition
patmatdbSearch a protein sequence with a motif
patmatmotifsSearch a PROSITE motif database with a protein sequence
pepcoilPredicts coiled coil regions
pregRegular expression search of a protein sequence
pscanScans proteins using PRINTS
sigcleaveReports protein signal cleavage sites

Protein mutation

Program nameWeb serviceDescription
msbarMutate sequence beyond all recognition
shuffleseqShuffles a set of sequences maintaining composition

Protein profiles

Program nameWeb serviceDescription
profitScan a sequence or database with a matrix or profile
prophecyCreates matrices/profiles from multiple alignments
prophetGapped alignment for profiles

Utils misc

Program nameWeb serviceDescription
embossversionWrites the current EMBOSS version number

W3htask

Program nameWeb serviceDescription
domainsweepIdentifies the domain architecture within a protein sequence
protsweepA Protein Identification Tool
twodsweep
 
 
2. SoapDB (rev. 2005/04) (WSDL) - Soap access to sequence databases at DKFZ:
 
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:
 
3. SoapGO (WSDL) - Soap access to GO (Gene Ontology) related methods:
 
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