To Obtain Accession Id From Genbank .Gbf Files

Question

[rosarylimyt]

Can anyone please help me with handling Genbank .gbf files? Recently I've generated Sequin (.sqn) files and Genbank (.gbf) files which I don't know what to do with them to obtain the accession IDs of the translated nucleotide sequences such that I know the names of the proteins identified. the .gbf files look something like this when I open with Notepad:

LOCUS       Scaffold1            1325603 bp    DNA     linear       14-FEB-2013
DEFINITION  No definition line found.
ACCESSION   
VERSION
KEYWORDS    .
SOURCE      Unknown.
  ORGANISM  Unknown.
            Unclassified.
FEATURES             Location/Qualifiers
     source          1..1325603
                     /organism="unknown"
                     /mol_type="genomic DNA"
     gene            complement(<1..555)
                     /locus_tag="asmbl_1"
     CDS             complement(<1..555)
                     /locus_tag="asmbl_1"
                     /codon_start=1
                     /transl_table=11
                     /product="tat (twin-arginine translocation) pathway signal
                     sequence domain protein"
                     /translation="MKEFHSTLSRRDFMKSLGVVGAGLGTMSAAAPVFHDLDEVTSST
                     LGINKNPWWVKERDFKNPTVPIDWSKVTRQPGVFQGLPRPTVADFTKAGVVGGTSTDL
                     ETPEMALTLYDAMAKEFPGWTPGYAGMGDTRTTALCNASKFMMFGAWPGNMEMGGKRV
                     NVIGAIMAAGGSPTFTPWLGPQLDT"
...
...

Does anyone here know of a software tool which I can use to make sense out of these and generate accession IDs for them?

Thank you in advance!

[Neilfws]

Not clear: this is a new .gbf, generated by you for some new sequence data? In which case there will not be any accessions or IDs; that happens after submission to GenBank and curation.

Answer 1

[Istvan Albert]

As Neilfws points out if this is your genbank file then there won't be any accession numbers, check your file for fields such as db_xref (see below):

 gene            1..626
                 /gene="Hbb-b1"
                 /gene_synonym="AA409645; beta1; HBB1; Hbbt1; Hbbt2"
                 /note="hemoglobin, beta adult major chain"
                 /db_xref="GeneID:15129"
                 /db_xref="MGI:96021"

If you do have those you can extract them in various ways, but before we get there let's make sure you have them in the first place.

[rosarylimyt]

No, I do not have the db_xref thing in the file. This .gbf file I got was generated from using CloVR-Search (annotation). Could you pls advise on how should I go about obtaining accession ID from it, apart from submitting to Genbank? Is there a program I can use to parse it such that I can isolate the 'translation=....' parts only? Thank you so much!

[Istvan Albert]

You will need to parse the file with a programming language, for example BioPython. See this section on parsing GenBank files: http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc36

[rosarylimyt]

Hi, I tried parsing one of the .gbf translated nucleotide scaffold with BioPython as advised via:

from Bio import SeqIO record=SeqIO.read('./rosary/dataset/clovr/Scaffold6.gbf','genbank'); record SeqRecord(seq=Seq('ATGGTGGGCCATCTTGGTCTCGAACCAAGGACCTCAGTCTTATCAGCTCCAACG...TGG', IUPACAmbiguousDNA()), id='', name='Scaffold6', description='No definition line found.', dbxrefs=[])

but it still wouldn't provide me with any sort of identification for that translated scaffold =[