[Bioperl-l] 1 small help with WU-BLAST -postsw

[Jason Stajich]

if you are really using Hit->frac_aligned I wouldn't rely on the Hit  
object frac_aligned - deal with the HSPs and calculate what you want  
- if there are multiple HSPs after a postsw some of those could be  
overalapping alternative sub-optimal alignments I don't know what  
thethe Hit object algorithm does when it tries to merge these examples.

My best advice is
  - find concrete examples of A,B and B,A pairs that doesn't meet  
your filter
  - print out the HSP information and LOOK at the HSPs and calculate  
the expected numbers by hand to figure out what is going on
  - there are going to be comparisons where it is ambiguous what  
would you do BY HAND for these cases, ignore them because they are  
the 5th best hit? take the longest HSP?   try and
    calculate overall coverage?
  - calculate frac aligned per HSP, decide what you want to do when  
there are multiple HSPs, take the longest, attempt to figure out some  
overall coverage, it all depends on your
  question if you are trying to find a single number
  - $hit_HSP_frac_aligned = $hsp->hit->length / $hit->length


Good luck.
-jason

On Jan 20, 2006, at 4:34 PM, Angshu Kar wrote:

> But I'm doing an AND.So if i do use alignment/hit > 0.5 and
> alignment/query > 0.5 as a filter will the length of the denominator
> matter?
>
> On 1/20/06, Jason Stajich <jason.stajich at duke.edu> wrote:
>> Well the hit and query probably are not the same length which is the
>> denominator in that fraction ....
>>
>> On Jan 20, 2006, at 1:57 PM, Angshu Kar wrote:
>>
>>> Hi,
>>>
>>> I'm using WU-BLASTP in yeast data (all vs all).
>>>
>>> Then I'm using :
>>>
>>> $hit_object->frac_aligned_query() > 0.5
>>> and
>>> $hit_object->frac_aligned_hit() > 0.5
>>>
>>> as filter conditions.
>>>
>>> In that I'm getting asymmetric results! I mean I've sequences A,B in
>>> my o/p and not B,A. Has it got something to do with the asymmetry of
>>> BLAST (but I thought -postsw takes care of that)?
>>>
>>> Please help.
>>>
>>> Thanks,
>>> Angshu
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Ignore the impossible but honor it ...
>>> The only enviable second position is success, since failure always
>>> comes first...
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>> --
>> Jason Stajich
>> Duke University
>> http://www.duke.edu/~jes12
>>
>>
>>
>
>
> --
> Ignore the impossible but honor it ...
> The only enviable second position is success, since failure always
> comes first...

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12/