Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.
org.embl.ebi.escience.scuflworkers.java.FlattenList
List HSOut = new ArrayList();
List RatOut = new ArrayList();
List MouseOut = new ArrayList();
Map hsToMouse = new HashMap();
Iterator j = MouseGeneIDs.iterator();
for (Iterator i = HSGeneIDs.iterator(); i.hasNext();) {
String id = (String)i.next();
hsToMouse.put(id, j.next());
}
Map hsToRat = new HashMap();
j = RatGeneIDs.iterator();
for (Iterator i = HSGeneIDs.iterator(); i.hasNext();) {
String id = (String)i.next();
hsToRat.put(id, j.next());
}
// Build the unique outputs
for (Iterator i = hsToRat.keySet().iterator(); i.hasNext();) {
String hsID = (String)i.next();
String ratID = (String)hsToRat.get(hsID);
// Remove version number
// ratID = (ratID.split("."))[0];
String mouseID = (String)hsToMouse.get(hsID);
// Remove version number
//mouseId = (mouseID.split("."))[0];
if (ratID != null && mouseID != null && ratID.equals("")==false && mouseID.equals("")==false) {
HSOut.add(hsID);
RatOut.add(ratID.split("\\.")[0]);
MouseOut.add(mouseID.split("\\.")[0]);
}
}
HSGeneIDs
MouseGeneIDs
RatGeneIDs
HSOut
RatOut
MouseOut
fasta = ">Human\n"+hsSeq+"\n>Mouse\n"+mmSeq+"\n>Rat\n"+rnSeq;
hsSeq
mmSeq
rnSeq
fasta
Reads and writes (returns) sequences
http://www.ebi.ac.uk/soaplab/emboss4/services/edit.seqret
Displays aligned sequences, with colouring and boxing
http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.prettyplot
Multiple alignment program - interface to ClustalW program
http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.emma
Homo sapiens genes (GRCh37)
Mus musculus genes (NCBIM37)
Rattus norvegicus genes (RGSC3.4)
Homo sapiens genes (GRCh37)
image/png
application/octet-stream
The array of png images returned from the plot processor
http://www.mygrid.org.uk/ontology#domain_concept