Get CDS from WGS fasta without annotate

Question

[雨]

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.

Answer 1

[colindaven]

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.

[雨]

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