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

Brian Osborne bosborne11 at verizon.net
Fri Sep 21 11:53:46 EDT 2007


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" <harryzs1981 at yahoo.com.cn> 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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