What Is The Best Orf Predictor For Plant Sequence?

Question

[maymay]

I know that there are different tools such as NCB ORF Finder, ORF Predictor, ESTScan, EMBOSS, Genscan, Anaconda that can be used for ORF prediction. From your experience, which one is best for predicting plant ORFs?

Answer 1

[klaas.vandepoele]

The FrameDP package is pretty useful, as it also includes a mode to correct frameshifts and can easily be re-trained for your species of interest. More info at https://iant.toulouse.inra.fr/FrameDP/

best regards, Klaas

Answer 2

[Monica M]

Check these out:

http://www.plantgdb.org/

http://genome.crg.es/geneid.html

http://bioinf.uni-greifswald.de/augustus/

If they don't your needs, check out the extensive list at: http://cmgm.stanford.edu/classes/genefind/

The Plant Genome Mapping Lab also has a nice list of resources, including software for gene prediction: http://www.plantgenome.uga.edu/links.htm

Good luck!

--monica

Answer 3

[x.jack.min]

If you deal with EST/CDS, give a try with OrfPredictor.

Answer 4

[SES]

For just finding ORFs, getorf and sixpack are the go-to tools in my stable. Those tools make it easy to select what type of ORF you want to analyze further, in a programmatic fashion. If you are more interested in gene prediction or alignment of ORFs, there are some other, more suitable tools, as others have mentioned.