Search a nucleotide sequence for tRNA genes using the tRNAscan-SE tool (see http://wiki.bioinformatics.org/TRNAscan-SE).
This workflow uses the tRNAscan service at VBI PathPort (see http://pathport.vbi.vt.edu/services/#predict_7).
Run tRNAscan.
http://pathport.vbi.vt.edu/services/wsdls/trnascan.wsdl
getTRNA
Get a fasta formated sequence for one of:
1. Actual sequence in an EMBOSS supported format (see http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in).
2. Sequence entry identifer in database:identifer format. Retreived using EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch).
3. An NCBI GI number. Retrived using NCBI's eUtils web service (see http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html)
Get a sequence in fasta format given one of:
1. An NCBI GI number (e.g. 75251068).
2. An entry identifier in database:identifier format (e.g. uniprot:Q96247).
3. A sequence entry in a format supported by EMBOSS seqret.
Fail is the sequence is not a GI number.
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
Fail if the sequence is a GI number.
org.embl.ebi.escience.scuflworkers.java.FailIfTrue
Is the input a GI number?
//
// Test if input is a GI number.
//
is_gi = "false";
try {
if(Integer.valueOf(gi_id_seq) > 0) {
is_gi = "true";
}
}
catch(NumberFormatException ex) {
is_gi = "false";
}
gi_id_seq
is_gi
Get the sequence in fasta format for a GI number.
Given an NCBI GI number get the sequence from the entry in fasta format. Uses the NCBI eUtils (see http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html).
Note: XPath is used instead of XML splitters to avaoid a problem with cyclic references in the XML.
//*[local-name(.)='eFetchResultMS']/*[local-name(.)='eFetchResult']/*[local-name(.)='TSeqSet']/*[local-name(.)='TSeq']
net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
//*[local-name(.)='TSeq']/*[local-name(.)='TSeq_defline']
net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
org.embl.ebi.escience.scuflworkers.java.StringListMerge
//*[local-name(.)='TSeq']/*[local-name(.)='TSeq_sequence']
net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
//*[local-name(.)='TSeq']/*[local-name(.)='TSeq_accver']
net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
fasta_seq = ">" + accver + " " + des + "\n";
fasta_seq += seq;
accver
des
seq
fasta_seq
org.embl.ebi.escience.scuflworkers.java.FlattenList
org.embl.ebi.escience.scuflworkers.java.FlattenList
org.embl.ebi.escience.scuflworkers.java.FlattenList
org.embl.ebi.escience.scuflworkers.java.FlattenList
org.embl.ebi.escience.scuflworkers.java.FlattenList
nucleotide
75251068
fasta
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl
run_eFetch_MS
NCBI GI number to get sequence from.
text/xml
Sequence in fasta format.
Sequence in XML format from eFetch.
Get fasta formated sequence for an entry identifer or a sequence entry.
Given a sequence or sequence entry identifer (e.g. uniprot:wap_rat), return the sequence in fasta format.
If a sequence identifier, in database:identifier format, is input the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the sequence in fasta format. Otherwise the input is assumed to be a sequence and if passed through the Soaplab EMBOSS seqret service to force the sequence into fasta format.
Fails if the workflow input is an identifier (i.e. is an actual sequence).
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
Fails if the workflow input was a sequence (i.e. is an identifer).
org.embl.ebi.escience.scuflworkers.java.FailIfTrue
Return true if the input is a sequence or false if the input is a sequence identifer (e.g. uniprot:wap_rat).
lineLen = sequence.indexOf("\n");
if(lineLen < 1) {
lineLen = sequence.length();
}
if(!sequence.startsWith(">") &&
sequence.indexOf(":") > 0 &&
sequence.indexOf(":") < lineLen) {
is_sequence = "false";
} else {
is_sequence = "true";
}
sequence
is_sequence
Fetch the sequence in fasta format from the identifer using EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch).
fasta
raw
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSDbfetch.wsdl
fetchData
Format sequence into fasta format.
fasta
http://www.ebi.ac.uk/soaplab/emboss4/services/edit.seqret
Either an actual sequence or an entry identifer in database:identifier format (e.g. uniprot:wap_rat).
Sequence in fasta format.
Completed
Fail_if_sequence
fetchData
Scheduled
Running
Completed
Fail_if_identifer
seqret
Scheduled
Running
Input sequence, GI number or entry identifier.
Sequence in fasta format.
Completed
Fail_if_GI
Sequence_or_ID
Scheduled
Running
Completed
Fail_if_sequence_or_id
Get_fasta_from_GI
Scheduled
Running
Input nucleotide sequence to search for tRNA genes. This can be one of:
- Actual sequence (fasta format recommended)
- Entry identifier in database:identifer format (e.g. EMBL:AB005233)
- NCBI GI number (e.g. 2264305)
The tRNAscan tool needs to know the type of tRNA signature to search for (e.g. Eukaryotic tRNAs).
Possible values are:
- Eukaryotic tRNAs
- Bacterial tRNAs
- Eukaryotic tRNAs
- Archaeal tRNAs
- Mitochondrial/Chloroplast tRNAs
- General tRNAs
text/xml
The tRNAscan result in the DAS XML format (see http://www.biodas.org/documents/spec.html).