Hi Perlmonks,

I am interested in extracting the name of genes from a NCBI Genbank file using accession number. Say, the accession number is NC_025572. When the accession number is used as a query in Nucleotide database of NCBI (https://www.ncbi.nlm.nih.gov/), it opens up a Genbank file with the title "Petrolisthes haswelli complete mitochondrial genome, isolate Mar55". In this file, the word CDS is repeated several times with a link and followed by information like <1..1534 /gene="COX1" or 1605..2289 /gene="COX2" or 2423..2773 /gene="ND3" etc. I have come across some perl codes from google search to extract the name from Genbank file. I have given the script below. It gives only the main title i.e. "Petrolisthes haswelli complete mitochondrial genome, isolate Mar55" and not the individual gene name like COX1 or COX2 or ND3. The digits prior to each gene name indicate position of sequence like 1..1534 or 1605..2289 or 2423..2773, respectively. I seek suggestions from perlmonks how to extract the gene name and its corresponding sequence for each gene. The output may look like:

>NC_025572 Gene COX1
ACGAAACGATGATTTTTTTCAACTAACCATAAGGATATTGGAACTTTATACTTTATTTTTGGAGCTTGAT
CGGGTATAGTAGGCACTACACTCAGATTAATTATTCGAACAGAACTCGGTCAGCCAGGTAGATTAATTGG
AGATGATCAGATTTATAATGTTGTTGTTACCGCCCACGCTTTCGTTATAATTTTTTTTATAGTTATACCA
ATCATAATTGGAGGATTTGGCAATTGACTAGTTCCTTTAATACTAGGAGCCCCTGATATAGCCTTTCCTC
GAATGAATAACATAAGATTTTGACTCCTACCTCCCTCGCTCACCCTACTTCTAATAAGAGGGATAGTTGA
AAGAGGAGTTGGTACTGGATGAACTGTCTACCCACCTCTATCAGCAGGTATTGCCCACGCAGGAGCATCA
GTTGATATAGGAATCTTTTCTCTCCATCTTGCAGGTGTTTCTTCTATTTTAGGAGCAGTTAACTTTATAA
CTACTGTTATTAATATACGACCCTCAGGAATGACTATAGACCGTATGCCATTATTTGTTTGGGCCGTATT
TATTACAGCTATTTTACTTTTATTATCTTTACCTGTTTTAGCAGGAGCCATCACAATACTTTTAACAGAT
CGTAATTTAAATACTTCCTTTTTTGACCCTGCTGGAGGAGGAGACCCTATTCTTTATCAACATCTTTTTT
GATTTTTTGGTCACCCCGAGGTTTATATTCTTATTCTTCCCGCATTTGGTATAATTTCACACATCGTAAG
TCAAGAATCAGGAAAAAAAGAGTCTTTTGGAACATTAGGTATGATTTACGCAATATTGGCTATTGGTATC
TTAGGTTTTATCGTTTGAGCACACCACATATTCACCGTTGGTATAGACGTTGATACACGAGCTTATTTTA
CATCAGCCACAATAATTATTGCCATCCCCACTGGAATTAAAATTTTCAGATGACTAGGAACGCTTCAAGG
AAACCAAATGAATTACAGACCTTCTATAGTCTGAGCTCTAGGTTTTATTTTTCTCTTTACAGTTGGAGGC
TTGACTGGTGTTATTTTAGCTAACTCTTCTATTGATACCGTACTACATGACACTTATTATGTAGTAGCTC
ACTTTCATTATGTTCTTTCAATAGGAGCTGTCTTCGGAATTTTTGCTGGTATTGCCCATTGATTTCCTCT
ATTTACTGGTGTTTCTACTAATCCTAAATGACTAAAAATCCATTTTTCAGTAATATTCCTAGGGGTAAAC
TTAACTTTCTTTCCTCAACACTTCCTTGGATTAAATGGAATACCTCGACGTTATTCTGATTATCCTGACG
CTTATACCCCATGAAACGTTTTATCTTCCGTTGGATCTTTAGTTTCTTTATGCGCAGTTATTGGTTTCAT
CTTTATTGTATGAGAAGCTCTAATTTCTTCACGACCTGTCTTATTTACCCTTTCTCAACCTACATCGATT
GAATGAAAACATCCTTATCCGCCCGCTGATCACAGATATATAGAAATTCCTATTCTTTCTAATT

>NC_025572 Gene COX2
ATGGCAACATGAGGTTCACTTGGTTTTCAAGATAGAGCATCTCCTTTAATGGAGCACCTTATTTACTTCC
ACGATCACGCGATAATTGTCCTTACCTTGATTACAGCCTTCGTGGGCTATATAATAATTTCCCTTTTACC
AAACACTTTTACAAATCGATTCCTTTTAGAAAATCAAAAGATTGAAATCATTTGAACTATTATCCCAGCT
TTCATTTTAGTTTTTATTGCTCTCCCCTCATTACGGCTTCTTTACCTTCTTGATGAAGTCAACAATCCAA
GAATTACTTTAAAAACCGTTGGCCATCAATGGTACTGGTCTTATGAATACTCCGATTTTCATCAAATTGA
ATTTGACTCTTATATAATCCAACCAAGAGATTCAGTAGACTCAACATTCCGTCTCATTGACGTTGACAAT
CGAGCAGTTTTACCAATAAATTCTCAAATTCGTGTACTAATTAGAGCCGCTGATGTAATTCATTCTTGAA
CCGTACCTGCTCTAGGAGTTAAAGCTGATGCTATCCCAGGCCGATTAAATCAAGTAAGATTCATAATTAA
CCGCCCAGGTTTATTTTTCGGTCAATGTTCTGAAATTTGCGGAGCTAATCACAGGTTTATACCTATTGTT
ATCGAAAGTGTTTCACTTGATTGTTTTCTAAAATGAGTGTCATCACAAGAAGAAT
[download]

Here goes the code:

 #!/usr/bin/perl
use warnings;
use strict;

use Bio::DB::GenBank;
use Bio::SeqIO; 
use Text::Wrap;
 
my $gb= new Bio::DB::GenBank;

my $acc="NC_025572"; 

my $seq1 = $gb->get_Seq_by_acc($acc);

my $desc=$seq1->desc();

print "\n $desc\n";  

exit;
[download]

I have got the following output from the script. It does not show name of individual gene.

 Microsoft Windows [Version 6.1.7600]
Copyright (c) 2009 Microsoft Corporation.  All rights reserved.

C:\Users\x>cd d*

C:\Users\x\Desktop>k.pl

 Petrolisthes haswelli complete mitochondrial genome, isolate Mar55.

C:\Users\x\Desktop>
[download]

I welcome suggestions from perlmonks to sort out this problem.