Question: open Reading Frame Prediction
0
gravatar for vishalchanda364
9 weeks ago by
vishalchanda36420 wrote:

Can CD-HIT tool be used for ORF Prediction? If not can anyone suggest me the best tool for the same.?

ADD COMMENTlink modified 9 weeks ago by ale_abd30 • written 9 weeks ago by vishalchanda36420

https://en.wikipedia.org/wiki/List_of_gene_prediction_software

ADD REPLYlink written 9 weeks ago by gb1.7k
1
gravatar for lieven.sterck
9 weeks ago by
lieven.sterck7.2k
VIB, Ghent, Belgium
lieven.sterck7.2k wrote:

No, CD-HIT can not do ORF prediciton, it's a sequence clustering/merging software.

For ORF prediction several tools exists. Some examples: FrameD, TransDecoder, longest_orf.pl, ...

For a more comprehensive list I suggest to use google.

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by lieven.sterck7.2k
1
gravatar for ale_abd
9 weeks ago by
ale_abd30
ale_abd30 wrote:

Hello, As far as I know, you cant use CD-HIT for such purpose. For ORF prediction I can suggest Prodigal or FragGeneScan both if you are working with prokaryotes. For Eukaryotic ORFs Glimmer HMM can be an option.

Good luck!

ADD COMMENTlink written 9 weeks ago by ale_abd30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1027 users visited in the last hour