[Biojava-dev] Percentage similarity

[Cleveland, John S]

Does anyone know how to retrieve the percentage similarity from a BLAST
result using BioJava?

 

This field is not available from SeqSimilaritySearchSubHit.
SeqSimilaritySearchSubHit does have the getEValue() and getScore()
methods, so I was a little confused about not finding the "percentage
identity" and "percentage similarity" fields.  I followed the directions
in http://biojava.org/wiki/BioJava:CookBook:Blast:Echo, but again the
percentage similarity does not seem to be getting parsed by the
BlastLikeSaxParser.  Here is the result of the aforementioned code:
 

startHit()

      HitProp:    subjectSequenceLength: 299

      HitProp:    subjectId: lcd|5392-AAA98259

      HitProp:    subjectDescription: 

startSubHit()

      SubHitProp: score: 24.6

      SubHitProp: expectValue: 6.9

      SubHitProp: numberOfIdentities: 14

      SubHitProp: alignmentSize: 42

      SubHitProp: percentageIdentity: 33

      SubHitProp: numberOfIdentities: 14

      SubHitProp: numberOfPositives: 23

      SubHitProp: queryFrame: plus1

      SubHitProp: querySequenceStart: 928

      SubHitProp: querySequenceEnd: 1047

      SubHitProp: querySequence:
TKDGKTQEWEMDNPGN--DFMTGSKDTYTFKLKDENLKIDDI

      SubHitProp: subjectSequenceStart: 126

      SubHitProp: subjectSequenceEnd: 167

      SubHitProp: subjectSequence:
TDDGKIREYELPNKGSYPSFITLGSDNALWFTENQNNAIGRI

endSubHit()

endHit()
 
 
Thanks,
John Cleveland