[Bioperl-l] embl sequences 2 fasta

[Pedro Antonio Reche]

Hi
I am interesting in finding all sequences from embl matching a given 
feature  in sub cellular location and then create a single file for 
each of them in fasta format. Any help will be appreciated.
Regards,

pedro

On Jun 30, 2005, at 5:55 PM, Josh Lauricha wrote:

> On Thu 06/30/05 16:48, Joseph Bedell wrote:
>> You can calculate the score given the bit score (from the tabular
>> output) and Lambda (calculated from the matrix). The equation is 
>> Score =
>> (Bits)/(Lambda in bits).
>>
>> Lambda is only dependent upon the matrix. Did you use NCBI-blast or
>> WU-BLAST? Which flavor of blast (blastn, blastp, etc)? In any case, 
>> you
>> can just run a single blast and look at the stats at the bottom of the
>> report to get the value of lambda. For example, a default NCBI-blastn
>> (+1/-3) search has a lambda of 1.37
>>
>> ============================
>> Lambda     K      H
>>     1.37    0.711     1.31
>>
>> Gapped
>> Lambda     K      H
>>     1.37    0.711     1.31
>> ===============================
>>
>> But, what is difficult to discover is this lambda is in NATS. To 
>> convert
>> it to bits, divide it by the natural log of 2, or in perl:
>>
>> perl -e 'print 1.37/log(2),"\n"'
>> 1.97649220601788
>>
>> So, now you can take all of your bit scores divided by 
>> 1.97649220601788
>> to get the Score.
>>
>> HTH,
>> Joey
>
> Cool, thanks. That'll save me a bunch of time ;) This was NCBI blastp,
> so I've already got it calculated ;)
>
> Thanks.
>
> -- 
>
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