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Re: To query Genbank online to get the sequence and annotations

by lin0 (Curate)
on May 31, 2007 at 18:26 UTC ( #618554=note: print w/ replies, xml ) Need Help??


in reply to To query Genbank online to get the sequence and annotations

Hi spring,

Welcome to the Monastery! After having a look at to your first two questions, it looks to me that you would benefit from having a look at the following nodes:

Now, back to your current question:

I am gonna find the Genbank DNA sequence with annotations given the genomic positions of certain DNA fragment. Is there a way to do this using Perl/Bioperl?

This is what I found by searching Google for perl Genbank DNA:

"GenBank (Genetic Sequence Data Bank) is a rapidly growing international repository of known genetic sequences from a variety of organisms. Its use is central to modern biology and to bioinformatics.

This chapter shows you how to write Perl programs to extract information from GenBank files and libraries. Exercises include looking for patterns; creating special libraries; and parsing the flat-file format to extract the DNA, annotation, and features. You will learn how to make a DBM database to create your own rapid-access lookups on selected data in a GenBank library.

Perl is a great tool for dealing with GenBank files. It enables you to extract and use any of the detailed data in the sequence and in the annotation, such as in the FEATURES table and elsewhere. When I first started using Perl, I wrote a program that searched GenBank for all sequence records annotated as being located on human chromosome 22. I found many genes where that information was so deeply buried within the annotation, that the major gene mapping database, Genome Database (GDB), hadn't included them in their chromosome map. I think you'll discover the same feeling of power over the information when you start applying Perl to GenBank files."

This is an extract from the Chapter 10 of Beginning Perl for Bioinformatics. The full chapter is available online

I hope this helps.

Cheers,

lin0


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