Re: [Biopython] Regarding blast record report
Peter Cock <[email protected]>
| Newsgroups | gmane.comp.python.bio.general |
|---|---|
| Message-ID | <CAKVJ-_43H_=B-s=9CwJ4GesdEmeHTWRoLQZc2aJhrMZHh2cvQQ@mail.gmail.com> |
The NCBI document their naming - although they have some much documentation is isn't always all up to date. https://www.ncbi.nlm.nih.gov/genbank/sequenceids/ GI stands for GenInfo Identifier, but is being deprecated so don't use it. Use the versioned accession if possible (the gb or ref entry in your example): https://ncbiinsights.ncbi.nlm.nih.gov/2016/07/15/ncbi-is-phasing-out-sequence-gis-heres-what-you-need-to-know/ The text after the identifier (after the first space) does seem to vary considerably depending on the BLAST database and where the sequence originally came from. Putting the species name in square brackets does seem to be a consistent NCBI pattern though. If you want more metadata about the sequence, rather than parsing this one line of text, it would be better to use the versioned accession to look this up directly, for example via NCBI Entrez. Peter On Thu, Nov 8, 2018 at 5:33 PM Ahmad Khalifa <[email protected]> wrote: > > 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 _______________________________________________ Biopython mailing list - [email protected] http://mailman.open-bio.org/mailman/listinfo/biopython