Question: converting ASN to Gff3
gravatar for mimi
9 months ago by
mimi20 wrote:


I used prospligh for protein alignment, but it gives as final file an ASN. It is not usable for data. I would like to convert it to gff3. Are there any tools to do this, can be on ncbi? But I searched, I did not find. thank you for helping me

ADD COMMENTlink modified 12 days ago by katharina.hoff50 • written 9 months ago by mimi20

what is prospligh ?

ADD REPLYlink written 9 months ago by Pierre Lindenbaum104k

ADD REPLYlink written 9 months ago by mimi20

Documentation says this. Looks like you can get a txt format file as well.

Run ProSplign with the compartment file and the fasta files to generate an alignment for each compartment (./prosplign -i comp -fasta subj.fa,query.fa -nogenbank -o pro.asn -eo pro.txt). The .asn file contains alignments in ASN format. The .txt file is designed for human reading.

When ProSplign is run without '-full' option, output file shows 'partial' alignments. A partial alignment is made from the full global alignment by throwing out low identity portions of the alignment and keeping conserved portions. The conserved portions are marked in text 'pro.txt' file with stars in the status line. Introns are marked with dots in the protein line

ADD REPLYlink modified 9 months ago • written 9 months ago by GenoMax42k
gravatar for katharina.hoff
12 days ago by
katharina.hoff50 wrote:

There is a asn2gff in the NCBI Toolkit (I have not tried using it, though).

ADD COMMENTlink written 12 days ago by katharina.hoff50
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