Extracting DNA sequences from GenBank files using Perl Post: 302328173

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Top Forums Shell Programming and Scripting Extracting DNA sequences from GenBank files using Perl Post 302328173 by akreibich07 on Tuesday 23rd of June 2009 03:28:18 PM

06-23-2009

Registered User

Extracting DNA sequences from GenBank files using Perl

Hi all,

Using Perl, I need to extract DNA bases from a GenBank file for a given plant species. A sample GenBank file is here...

Nucleotide

This is saved on my computer as NC_001666.gb. I also have a file that is saved on my computer as NC_001666.txt. This text file has a list of all the genes and their positions in the species corresponding to NC_001666 (corn). Here is a sample of how the text file is formatted...

rbcL (56874..58304)
atpB -(54618..56114)
atpE -(54208..54621)
trnM (54020..54092)
trnV -(53158..53834)

For example, if in my command prompt I give input of the program name, the species number that I want, and the specific gene from that species whose DNA sequence I want:

perl nucleotide_bases.pl NC_001666 trnM

The program would go into NC_001666.txt, find trnM, see that it has a range from 54020 to 54092 and is on the positive strand(no negative sign). The program then goes into NC_001666.gb, goes to the long list of DNA bases at the bottom and starts at position 54020 and returns all base letters through 54092 (inclusively). So for this specific trnM, the output would be:

gcctacttaactcagtggttagagtattgctttcatacggcgggagtcattggttcaaatccaatagtaggta

If a gene has a negative next to the position range (meaning it's on the negative strand of DNA), the output should be reversed, starting from the higher position, going to the lower. Also, when a negative is there, in that output, all A's should be switched to T's, and all G's to C's and vice versa.

Also, if a gene appears more than once in a text file, give an error message that it appears more than once, and end the program.

If I could get a Perl script to return this information for any species (NC_number) I want, and any gene from that species that I want, it would be a great help in the research I am conducting. Thank you all for your time, and any help on how to write this script would be appreciated.

-akreibich07

akreibich07

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LEARN ABOUT DEBIAN

gbseqget

GBSEQGET(1)						     NCBI Tools User's Manual						       GBSEQGET(1)

NAME

       gbseqget - format sequences from GenBank as an XML GBSet

SYNOPSIS

       gbseqget [-] [-d filename] [-i filename] [-m n/p/b] [-n] [-o filename] [-v]

DESCRIPTION

       gbseqget  retrieves  biological sequence data from GenBank (according to an input list of GI accession numbers) and prints it out as an XML
       GBSet document.

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -d filename
	      Input file name for date list (desired accessions, one per line, followed by a blank line and a list of allowed dates, also one  per
	      line)

       -i filename
	      Input file name for GI list (default = stdin)

       -m n/p/b
	      Molecule type:
	      n      Nucleotide (default)
	      p      Protein
	      b      Both

       -n     Return only new records (for which the given GI refers to an old version)

       -o filename
	      Output file name for the XML GBSet (default = stdout)

       -v     Fetch SNP Variations

NOTES

       The GBSet format is deprecated in favor of INSDSet, which you can produce by running insdseqget in place of gbseqget.

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       asn2gb(1), insdseqget(1).

NCBI
								    2006-04-14							       GBSEQGET(1)