[Bioperl-l] computing gc content of a list of sequences

[Smithies, Russell]

Try bp_gccalc.pl

[smithiesr at impala ~]$ bp_gccalc.pl temp/sequences.fasta
Seq: 1  Len:149
GC content is 0.8255
Number of bases of type A= 22
Number of bases of type C= 49
Number of bases of type G= 74
Number of bases of type T= 4
--
Seq: 2  Len:5022
GC content is 0.5014
Number of bases of type A= 1282
Number of bases of type C= 1212
Number of bases of type G= 1306
Number of bases of type T= 1222
--
Seq: 3  Len:4923
GC content is 0.5452
Number of bases of type A= 1143
Number of bases of type C= 1307
Number of bases of type G= 1377
Number of bases of type T= 1096

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Emanuele Osimo
> Sent: Friday, 2 October 2009 5:42 a.m.
> To: perl bioperl ml
> Subject: [Bioperl-l] computing gc content of a list of sequences
> 
> Dear all,
> I have a multifasta file with a list of sequences.
> How can I compute the gc % content of each of them? Is there a Bioperl tool?
> Thanks
> Emanuele
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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