[Bioperl-l] Find tiling path

[michael watson (IAH-C)]

Hi

Thank you, sequence assembly will come after the step I am talking about
:-)

What I have is about 30,000 sequences, perhaps only 100 of which span
the region I want to create a contig for.  The step I am talking about
is identifying, out of the 30,000 sequences, those that match to the
region I want to contig - and only being in posession of the sequences
at one or both ends of that contig i.e. I want to start with a sequence
at the 5' end, and kind of "walk" along the sequence in the 3' direction
by identifying hits in the database that take me in that direction

Thanks
Mick

-----Original Message-----
From: Remo Sanges [mailto:sanges at biogem.it] 
Sent: 18 June 2004 14:40
To: michael watson (IAH-C)
Cc: BioPerl-List
Subject: Re: [Bioperl-l] Find tiling path


On Jun 18, 2004, at 3:29 PM, michael watson (IAH-C) wrote:

> Quick question:
>
> I have a database of sequences.  One of my queries hits one sequence 
> in the DB, another hits a different sequence in the DB.  I have reason

> to believe that other sequences in the DB will form a "tiling path" 
> between sequence 1 and sequence 2 so I can create a contig that spans 
> the gap. Is there something which does that?  I'm using BLAST as my 
> query algorithm.

You can try Cap3
http://genome.cs.mtu.edu/cap/cap3.html
or Phrap
http://phrap.org/

Remo