Question: annotate gene feature
0
gravatar for arunprasanna83
6 weeks ago by
arunprasanna8330 wrote:

Hi,

I have a multi-fasta file with >15k DNA sequences. I wish to mark, UTR's, start, stop features. I tried expasy translate tool and it gives translated sequence with different possible ORFs. My objective is to find, how many sequences are full length. Kindly suggest.

Thanks.

utr feature annotation gene • 124 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by arunprasanna8330

Is this for genome annotation? If so, there are many resources for structural annotation of a genome on biostars to search for.

ADD REPLYlink written 6 weeks ago by jean.elbers1.1k
1
gravatar for arunprasanna83
6 weeks ago by
arunprasanna8330 wrote:

It is for multiple purpose. This is basically a isoseq data. So need to confirm how many of them are full length transcripts.

ADD COMMENTlink written 6 weeks ago by arunprasanna8330

Perhaps you could try

Tool: pinfish: tools to annotate genomes using long read transcriptomics data pinfish: tools to annotate genomes using long read transcriptomics data

and maybe also Transcriptome Annotation by Modular Algorithms (for Iso-Seq data) https://github.com/GenomeRIK/tama

This tool from EMBOSS might also be useful http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/getorf.html

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by jean.elbers1.1k
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