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Is there a tool for converting GenBank sequin format data (.sqn) into the gff3 format? I have a number of .sqn format annotations that I need to get into gff3 for some other tools I'd like to run. I could also use bed format, so a sequin to bed converter would work too.
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Not in a single step that I know of. But NCBI has converters from Sequin ASN.1 format to other formats. asn2gb will convert to a Genbank flatfile,
ftp://ftp.ncbi.nih.gov/toolbox/ncbi_...rogram/asn2gb/
and then it looks like there are various options (search for "gb2gff") to finish the conversion.
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