Question

open Reading Frame Prediction

0

Entering edit mode

4.3 years ago

vishalchanda364 ▴ 20

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

Assembly genome next-gen alignment • 887 views

ADD COMMENT • link updated 4.3 years ago by ale_abd ▴ 50 • written 4.3 years ago by vishalchanda364 ▴ 20

0

Entering edit mode

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

ADD REPLY • link 4.3 years ago by gb ★ 2.2k

score 1 · Answer 1 · 2020-01-27

1

Entering edit mode

4.3 years ago

lieven.sterck 15k

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 COMMENT • link 4.3 years ago by lieven.sterck 15k

score 1 · Answer 2 · 2020-01-27

1

Entering edit mode

4.3 years ago

ale_abd ▴ 50

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 COMMENT • link 4.3 years ago by ale_abd ▴ 50