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Old 05-15-2012, 08:58 AM   #1
Location: san diego

Join Date: Jan 2012
Posts: 38
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?
ashuchawla is offline   Reply With Quote
Old 05-15-2012, 09:07 AM   #2
Location: Sweden

Join Date: Jan 2012
Posts: 45

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
Krish_143 is offline   Reply With Quote
Old 05-15-2012, 11:01 AM   #3
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Location: Denmark

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Here is how this can be done with Biopieces:

read_genbank -i |
grab -k PRODUCT -p '16S ribosomal RNA' |
rename_keys -k PRODUCT,SEQ_NAME |
write_fasta -x
read_embl can be used for embl files.
maasha is offline   Reply With Quote
Old 05-16-2012, 07:00 AM   #4
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
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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:
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