[Biopython] Regarding blast record report
Ahmad Khalifa <[email protected]>
| Newsgroups | gmane.comp.python.bio.general |
|---|---|
| Message-ID | <CAL1o8vOkFgb5EOOZ84bcTy7Y8w7o1O48Z3_E4JcKn=YrUpZhLQ@mail.gmail.com> |
Hello, I want to extract certain information from the biopython blast output. In the header I often get variable amounts of information in the title, for example: gi|1335041855|gb|PNW76469.1| hypothetical protein CHLRE_11g467616v5 [Chlamydomonas reinhardtii] gi|159481404|ref|XP_001698769.1| predicted protein [Chlamydomonas reinhardtii] >gi|745998015|sp|A8JA42.1|IFT56_CHLRE RecName: Full=Intraflagellar transport protein 56; AltName: Full=Abnormal dye filling protein 13; AltName: Full=Tetratricopeptide repeat protein 26 homolog; Short=TPR repeat protein 26 homolog gi|1335043717|gb|PNW78329.1| hypothetical protein CHLRE_09g401700v5 [Chlamydomonas reinhardtii] I wonder what exactly is contained in this output, what's gi and gb? How come sometimes I have a refseq or a uniprot accession code but not always (the same information is not consistently present, very difficult to mine). Is it possible to retrieve a uniprot accession code for my hits or a gene name that I can map to an accession code using uniprots API? What I really want is to mine the title to get every piece of information separately (if it exists of course), are there parsers that do that? Best regards. _______________________________________________ Biopython mailing list - [email protected] http://mailman.open-bio.org/mailman/listinfo/biopython