Gene ID conversion and Pathway analysis after mosquito blast

Question

[super]

Hi all

I have got my blast result from mosquito Contigs Fasta format.

Something like

query_name query_length accession_number
1059N_ae_contig_1 676 XM_001650645
1059N_ae_contig_5 563 XM_001650988
1059N_ae_contig_6 2123 XM_001664234

I want to do the pathway analysis on this genes. However, the GenBank accession number is not suitable for the further analysis.

1. Any one knows how to do that?
2. I could transfer the mosquito GenBank accession ID to Vectorbase ID. But I don't know how could I transfer them automatically.
3. Or Could I just blast the contigs to human/mouse and get the gene name and then go to GO/pathway analysis? Is it reasonable?

Thank you!

Answer 1

[Joseph Hughes]

Hi,

This Bioperl script using the Eutilities module gives you the vector base ID for a given accession number, you could create a loop to automate this for multiple accession numbers:

use Bio::DB::EUtilities;
use Bio::SeqIO;

my @ids = qw(XM_001656826.1);

my $factory = Bio::DB::EUtilities->new(-eutil   => 'efetch',
                                       -db      => 'protein',
                                       -rettype => 'gb',
                                       -email   => '[e-mail]',
                                       -id      => \@ids);

my $file = 'myseqs.gb';

$factory->get_Response(-file => $file);

my $seqin = Bio::SeqIO->new(-file   => $file,
                            -format => 'genbank');

while (my $seq = $seqin->next_seq) {
 print $seq->id();
 for my $feat_object ($seq->get_SeqFeatures) {          
   if ($feat_object->primary_tag=~/CDS/){
     for my $tag ($feat_object->get_all_tags) {             
        if ($tag=~/db_xref/){            
        for my $value ($feat_object->get_tag_values($tag)) {                
           if ($value=~/VectorBase/){
             print "\t$value"
           }
        }     
      }     
     }  
   }     
  }
}

[super]

It is very helpful!