[Bioperl-l] =?gb2312?q?=BB=D8=B8=B4=A3=BA=20Re:=20=20Help=20for=20extracti?= =?gb2312?q?ng=20CDS=20sequences=20from=20FASTA=20form?=

sheng zhao harryzs1981 at yahoo.com.cn
Fri Sep 21 12:32:21 EDT 2007


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> дµÀ£º
  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 
> 
> 
> 
> 
> 
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