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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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  • 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:
    http://emboss.open-bio.org/wiki/Appdoc:Seqret

    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:

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

    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?
    Tags: None
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