[Biojava-l] creating a sequence...

Jan Würthner jan.wuerthner at uni-duesseldorf.de
Thu Jan 29 15:54:26 EST 2004

Sorry for answering the email myself...

after looking at it again, I think it is adequate to treat these three 
elements (query-ID, query-def and query-len) as annotations. There is no 
sense in assigning them to an unknown sequence, right?

I have implemented it this way and it works fine,
thanks anyway

kind regards

Am Thursday 29 January 2004 20:23 schrieb Jan Würthner:
> 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
Universitätsstraße 1
40225 Duesseldorf

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

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