This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Get CDS from WGS fasta without annotate

I use a mature mRNA sequence (cds) to blast in an unannotated genome, because of the presence of introns, we get several exon fragments, how do I extract them and organize them into a complete cds?The genome has no gff3 files, only gbff files.

blast
• 966 views • link
updated by Ram Ram • written by 雨 • 雨

1 answer

You can take your mRNA FASTA files, and map to the genome with gmap. Use the GFF3 output option.

You're not going to get anywhere with BLAST.

For a full reannotation, try Maker.

Else you could try converting your GBFF files, whatever they are.

• 0 views • link
written by colindaven colindaven

thanks a lot.I will try the way you said.

• 0 views • link
written by 雨 • 雨

Log in to answer this question.

More posts like this