[Bioperl-l] bl2seq of NCBI

Mane, Ajay (UMR-Student) amtd9 at umr.edu
Tue Mar 15 17:04:07 EST 2005

I am new to bioperl. I want to use the bl2seq tool of NCBI giving the input query sequences in a perl script.
I have gone through the documentation, but not clear how to start. Can anyone send a sample perl script which 
uses the bl2seq tool. What all needs to be installed.


From: bioperl-l-bounces at portal.open-bio.org on behalf of Stefan Kirov
Sent: Tue 3/15/2005 3:46 PM
To: Mingyi Liu
Cc: bioperl-l at portal.open-bio.org; Andrew Dalke
Subject: Re: [Bioperl-l] Error reporting/Validation implemented

Few things:
I used your parser to produce Bioperl objects based on some of the high
level features and compared it ot what I have. Your parser is
considerably faster (about twice), but it is still hard to tell as I am
descending further  in the hierarchy with mine. At the same time I don't
think the difference will vanish, so I will start building over your
parser to produce bioperl objects. I am not sure exactly how I am going
to deal with the relationships that are necessary, but I'll deal with it
when I finsih everything else.
By the way it took 9 minutes on a 64 bit Xeon  3.4GHz even with Bioperl
objects construction on the whole Homo_sapiens ASN file. The data that
went inside the objects was: general desc of the genes (symbol, name,
summary, etc.), organsism descr. but none of the truly big parts.
Unfortunately, I am leaving tomorrow for a conference, so I will have
some more next week earliest. Thanks for sharing the code!

Mingyi Liu wrote:

> Hi, there,
> I just implemented basic error reporting and validation
> functionalities in my Entrez Gene parser in Perl (the regex version). 
> The validation will catch all non-conforming data, while error
> reporting reports line number, error type, and the first 20
> (customizable) characters of the offending data (but the line number
> could be incorrect if the format resulted in an exception, which is
> hard to deal with for ASN.1-formatted data, although easy for XML
> parsers).
> The speed for the parser of course slowed down, but I'd say it'd still
> beat most parsers hands down.  The full human genome now takes a bit
> over 12 minutes instead of 11 minutes to process on one Intel Xeon 2.4
> GHz CPU.  So I don't think my parser's speed has much to do with
> performing validation or not.
> I had also communicated with Stefan Kirov and turns out the dead
> entries and 0-sized (should be 1-sized) arrays were simply related to
> data trimming options.  So far, so good.
> If anyone is interested, check it out at
> http://www.sourceforge.net/projects/egparser/.
> Regards,
> Mingyi
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