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

gopu_36 gopu_36 at yahoo.com
Sat Mar 14 22:38:31 EDT 2009


Hi Jason,
Thanks for your help.

I did try as below for testing purpose:

blat  database.fa query.fa output.psl
blat  database.fa query.fa output.blast

Both the results looks the same and the output.blast also lokks lo=ike
normal psl format. As I have always used .psl format, I am not sure what the
problem while getting the blast like output? Could you please let me know? 
Thanks you so much.


Jason Stajich-3 wrote:
> 
> 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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