1. embl/gbk to FASTA conversion; 2. 16s RNA to be found in a embl/gbk file

[ashuchawla]

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?

[Krish_143]

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

[maasha]

Here is how this can be done with Biopieces:

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.

[maubp]

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