[Bioperl-l] BLAT Howto?

Heikki Lehvaslaiho heikki.lehvaslaiho at gmail.com
Wed Jul 7 13:14:21 EDT 2010


There are BLAT and SSAHA that have been around for some time. For next
gen sequences, there are more algorithms coming up all the time.
Have a look at e.g. Li and Homer in Briefings in Bioinformatics "A
survey of sequence alignment algorithms for next-generation
sequencing".


     -Heikki


On 28 June 2010 16:15, Minh Bui <buiduyminh at gmail.com> wrote:
> Hi everyone,
> I am new to Bioperl and perl itself and running perl on window 7.
>
>  My job is to develop an application that can search through a  database
> with thousands of queries. BLAT is a  best option (if you know any other
> algorithm that can do this, please let me know). I have been searching
> through Bioperl BLAT documentation and there is only one document for BLAT
> but without example.
> I am wondering if anyone has done BLAT using Bioperl, please show me how to
> use BLAT in  Bioperl.
>
> Thank you very much and sorry for my english. Its not my first language.
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