[Bioperl-l] script to calculate percentage identity for BLAT psl

Jason Stajich jason at bioperl.org
Sat Mar 14 21:11:01 EDT 2009


well you could just output it in blast9 output and then the 3rd column  
is percent identity.

On Mar 14, 2009, at 6:04 PM, gopu_36 wrote:

>
> Please let me know whether any other way of calculating the precentage
> identity for commandline BLAT results? . Thanks.
>
> gopu_36 wrote:
>>
>> Hi,
>>
>> I did go through FAQ from BLAT on how to calculate the precentage  
>> identity
>> from http://genome.ucsc.edu/FAQ/FAQblat#blat4
>> As a new comer, I don;t usederstand on how to implement this.  
>> Please let
>> me know how to plugin the script for my output.psl file. Please let  
>> me
>> know. It would be of great help.
>>
>> Thanks and Regards.
>>
>
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Jason Stajich
jason at bioperl.org





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