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 Homo sapiens genes (NCBI36) Mus musculus genes (NCBIM36) Rattus norvegicus genes (RGSC3.4) Homo sapiens genes (NCBI36) 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 (NCBI36) image/png application/octet-stream The array of png images returned from the plot processor http://www.mygrid.org.uk/ontology#domain_concept