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  • maubp
    replied
    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:

    Leave a comment:


  • maasha
    replied
    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.

    Leave a comment:


  • Krish_143
    replied
    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

    Leave a comment:


  • 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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