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

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  • 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?

  • #2
    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
    Krishna

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    • #3
      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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      • #4
        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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