Starts by fetching all gene IDs from Ensembl corresponding to human genes on chromosome 22 implicated in known diseases and with homologous genes in rat and mouse. For each of these gene IDs it fetches the 200bp after the five prime end of the genomic sequence in each organism and performs a multiple alignment of the sequences using the EMBOSS tool 'emma' (a wrapper around ClustalW). Returns PNG images of the multiple alignment along with three columns containing the human, rat and mouse gene IDs used in each case. 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 org.embl.ebi.escience.scuflworkers.java.FlattenList fasta = ">Human\n"+hsSeq+"\n>Mouse\n"+mmSeq+"\n>Rat\n"+rnSeq; hsSeq mmSeq rnSeq fasta Fetch disease genes with homologues in mouse, get the rat IDs as well. Note that this therefore results in rows in the output with empty rat gene IDs as the current XML ui definition doesn't allow us to define more than one species specific filter (hopefully this will be fixed). This is corrected by the downstream beanshell script which removes these empty rows. hsapiens_gene_ensembl hsapiens_gene_ensembl rnorvegicus_gene_ensembl mmusculus_gene_ensembl Reads and writes (returns) sequences http://www.ebi.ac.uk/soaplab/services/edit.seqret Displays aligned sequences, with colouring and boxing http://www.ebi.ac.uk/soaplab/services/alignment_multiple.prettyplot Multiple alignment program - interface to ClustalW program http://www.ebi.ac.uk/soaplab/services/alignment_multiple.emma mmusculus_gene_ensembl scerevisiae_gene_ensembl uniprot image/png application/octet-stream The array of png images returned from the plot processor http://www.mygrid.org.uk/ontology#domain_concept