Question: converting ASN to Gff3
1
gravatar for mimi
11 months ago by
mimi20
mimi20 wrote:

Hello,

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 10 weeks ago by katharina.hoff50 • written 11 months ago by mimi20

what is prospligh ?

ADD REPLYlink written 11 months ago by Pierre Lindenbaum106k

https://www.ncbi.nlm.nih.gov/sutils/static/prosplign/prosplign.html

ADD REPLYlink written 11 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 11 months ago • written 11 months ago by genomax46k
0
gravatar for katharina.hoff
10 weeks ago by
Germany
katharina.hoff50 wrote:

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

ADD COMMENTlink written 10 weeks ago by katharina.hoff50
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