[Bioperl-l] How to get protein ID and get protein accession from GI

bill at genenformics.com bill at genenformics.com
Thu Jun 5 01:16:07 EDT 2008


Hi, Ousmane,

IdConvert, a standalone application which convert protein/nucleotide
gi/acc, can be freely downloaded from
http://www.genenformics.com/download.html

A sample output is available at
http://www.genenformics.com/IdConvert_example_result.txt

The following is a test run:
>IdConvert.exe 300,NM_005252,399,NP_001225
#Input	Nuc_GI	Nuc_Acc	Pro_GI	Pro_Acc	Desc
300	299	X59693.1	300	CAA42214.1	ubiquinol--cytochrome c reductase [Bos
taurus]
NM_005252	6552332	NM_005252.2	4885241	NP_005243.1	v-fos FBJ murine
osteosarcoma viral oncogene homolog [Homo sapiens]
399	399	V00111.1	400	CAA23445.1	unnamed protein product [Bos taurus]
NP_001225	15451858	NM_001234.3	4502589	NP_001225.1	caveolin 3 [Homo sapiens]

Bill at genenformics.com



> hello,
> Could somebody help me on how to get the protein ID and ACCESSION using
> the mRNA gi or accession.
>
>
> my $db_obj = Bio::DB::GenBank->new();
> my $seq_obj = $db_obj->get_Seq_by_acc('123456') ;   # I pass here the mrna
> acc to get the seq_obj
> my $gi = $seq_obj->primary_id ;                     # I get here the gi
>
>
> I need to get the protein ID and protein ACCESSION"
>
> THANKS!!
>
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> Bioperl-l at lists.open-bio.org
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>




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