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To query Genbank online to get the sequence and annotations

by spring (Novice)
on May 31, 2007 at 15:49 UTC ( #618522=perlquestion: print w/ replies, xml ) Need Help??
spring has asked for the wisdom of the Perl Monks concerning the following 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? I use Perl pretty light, so please help! thanks.

Comment on To query Genbank online to get the sequence and annotations
Re: To query Genbank online to get the sequence and annotations
by lin0 (Curate) on May 31, 2007 at 18:26 UTC

    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
Re: To query Genbank online to get the sequence and annotations
by erix (Vicar) on Jun 01, 2007 at 20:13 UTC

    Depending on how deeply you want to go into the programming, there are several perl approaches; the following depend on having bioperl installed.

    And if you want to go the BioPerl route, make sure you use a recent version, like 1.5.2 (nevermind the 'developer version' comment on that page). For searching GenBank, just read the HOWTO's:

    Bioperl Beginners HOWTO

    Bioperl SeqIO HOWTO

    An alternative may be BioMart (see esp. the martview button). BioMart lets you click together your query interactively, which in itself is already useful. But on top of that you can get the same query in xml form by clicking the XML button, and saving the query (not the data) in xml format. The retrieved query-xml can then be re-submitted programmatically, possibly after tweaking it. This makes it pretty easy to get started submitting queries to this specialized database.

    The most control you get by using the ensembl perl API (see perl API installation page). This API lets you connect to the mysql servers at ebi (or you can download data & install it locally).

    An ensembl perl API tutorial, scratching the surface deeply, is here: ensembl Core perl API tutorial.

    Ensembl and BioMart have basically the same data (although there are some differences), with biomart being a denormalized version of the master data in ensembl.

    Needless to say, there is a lot of annotation/cross-references/expertise at ebi, and this is built into these API's.

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