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Old 05-15-2012, 09:58 AM   #1
ashuchawla
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Default 1. embl/gbk to FASTA conversion; 2. 16s RNA to be found in a embl/gbk file

I need help with 2 things:

1. I have a EMBL or a gbk file format for the contigs of Salmonella enterica and I want to find the contig that has 16sRNA gene. Could anybody help me with this please?

2. How can I convert EMBL/gbk to FASTA format?
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Old 05-15-2012, 10:07 AM   #2
Krish_143
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If you have gff file and genome file, then you can extract fasta format sequences in many ways. here i know using Cufflinks source.
gffread -E annotation.gff -o- | more
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Old 05-15-2012, 12:01 PM   #3
maasha
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Here is how this can be done with Biopieces:

Code:
read_genbank -i E_coli_K12_MG1655.gb |
grab -k PRODUCT -p '16S ribosomal RNA' |
rename_keys -k PRODUCT,SEQ_NAME |
write_fasta -x
read_embl can be used for embl files.
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Old 05-16-2012, 08:00 AM   #4
maubp
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Quote:
Originally Posted by ashuchawla View Post
How can I convert EMBL/gbk to FASTA format?
EMBOSS seqret will convert from EMBL to FASTA, GenBank to FASTA, etc:
http://emboss.open-bio.org/wiki/Appdoc:Seqret
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