[Biojava-l] creating a sequence...

Jan Würthner jan.wuerthner at uni-duesseldorf.de
Thu Jan 29 14:23:54 EST 2004


I have written a BlastParser for xml based BLAST results, in order to 
reconstruct SeqSimilaritySearchResult instances from xml files returned by 
the NCBI for BLAST requests.

In constructing the searchresult, I use

SequenceBuilder sb = new SimpleSequenceBuilder();
SeqSimilaritySearchResult result
    = new SimpleSeqSimilaritySearchResult( sb.makeSequence(),
							  new DummySequenceDB("dummy"),
							  new SimpleAnnotation(annotations));
where hits is a List of SeqSimilaritySearchHits and searchParameters and 
annotations are Maps.

The XML file still contains information about the query, like ID and length, 
but not the whole query sequence, e.g.:

  <BlastOutput_query-def>Mus musculus serum amyloid A protein isoform 2 mRNA, 
complete cds</BlastOutput_query-def>

Here is my question:

How can I adopt this information into the SimpleSeqSimilaritySearchResult? The 
sequence I obtain by


of course does not contain anything. Is there a way to construct a sequence by 
the query-ID, query-def and query-len? (Especially the length is something I 

Thanks in advance

Jan Würthner
Institute for Medical Microbiology
Building 22.21
Universitätsstraße 1
40225 Duesseldorf

Tel. +49 (0) 211 81 12461
URL: www.medmikro.uni-duesseldorf.de

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