Hi,
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"),
searchParameters,
hits,
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-ID>gi|1698579|gb|U60438.1|MMU60438</BlastOutput_query-ID>
<BlastOutput_query-def>Mus musculus serum amyloid A protein isoform 2 mRNA,
complete cds</BlastOutput_query-def>
<BlastOutput_query-len>576</BlastOutput_query-len>
Here is my question:
How can I adopt this information into the SimpleSeqSimilaritySearchResult? The
sequence I obtain by
sb.makeSequence()
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
need!)
Thanks in advance
Jan
--
Jan Würthner
Institute for Medical Microbiology
Building 22.21
Heinrich-Heine-University
Universitätsstraße 1
40225 Duesseldorf
Tel. +49 (0) 211 81 12461
URL: www.medmikro.uni-duesseldorf.de
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