[Bioperl-l] 回复： Re: Help for extracting CDS sequences from FASTA form

[sheng zhao]

Dear Brian O.:
   
   Thank you for your reple.
  I just want to get CDS sequences (DNA sequence) from them according to the CDS information in the title for each sequence. 
   
  For example, for the first sequence, the information is "complete cds /cds=p(18,452)" .

  Thank you again!
   
  Best wishes!
  Harry



Brian Osborne <bosborne11 at verizon.net> 写道：
  Harry,

Do you mean find an ORF starting at the first initiation codon and translate
that? Or some other approach?

Take a look at the translate() method:

http://www.bioperl.org/wiki/Bptutorial.pl#Translating


Brian O.


On 9/21/07 10:40 AM, "sheng zhao" wrote:

> Dear all:
> I have got a set of DAN sequences in FASTA form as following:
> 
>> gnl|UG|Bt#S37443275 Bos taurus cathelicidin 4, mRNA (cDNA clone MGC:157131
>> IMAGE:8442308), complete cds /cds=p(18,452) /gb=BC133480 /gi=126717494
>> /ug=Bt.3 /len=572
> 
> TAGGCAGACTGGGGACCATGCAAACCCAGAGGGCCAGCCTCTCACTGGGGCGGTGGTCAC..................
> ................
>> gnl|UG|Bt#S11932596 B.taurus mRNA for interleukin-5 /cds=p(1,405) /gb=Z67872
>> /gi=1113120 /ug=Bt.5 /len=405
> 
> TAGGCAGACTGGGGACCATGCAAACCCAGAGGGCCAGCCTCTCACTGGGGCGGTGGTCAC..................
> .................
>> gnl|UG|Bt#S29311270 Hw_Loin_11_0520_C11 Bos taurus CF-24-HW loin cDNA library
>> Bos taurus cDNA, mRNA sequence /gb=DV796078 /gi=82648993 /ug=Bt.10 /len=1332
> 
> AACCGGGAGCACGCCGTGTACCCGCCAGTGGGGCTTCTGAGGACATGGGGGCCACCGTCA..................
> .................
> 
> I would like to know how to extract CDS sequences from them? Or a Perl
> program?
> 
> Thank you for your reply and help.
> 
> Sincerely yours,
> Best wishes,
> Harry 
> 
> 
> 
> 
> 
> ---------------------------------
> @yahoo.cn 新域名、无限量，快来抢注！
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




       
---------------------------------
雅虎邮箱，终生伙伴！