Question

Gene prediction tool

0

Entering edit mode

5.9 years ago

naveenram2205 • 0

Is there any gene predction tool that using transcriptome, translatome, proteome databases to predict gene?

gene • 1.7k views

ADD COMMENT • link updated 5.9 years ago by Erin Haskell ▴ 470 • written 5.9 years ago by naveenram2205 • 0

0

Entering edit mode

Thank you sir. i"ll try that

ADD REPLY • link 5.9 years ago by naveenram2205 • 0

score 2 · Answer 1 · 2019-02-14

2

Entering edit mode

5.9 years ago

JC 13k

You can train Augustus with that information

ADD COMMENT • link 5.9 years ago by JC 13k

score 0 · Answer 2 · 2019-02-14

0

Entering edit mode

5.9 years ago

Charles Warden 8.3k

You might also want to consider MAKER (which can use different data sources) or Exonerate (doesn't use different data sources, but can be tested for making gene annotations)

ADD COMMENT • link 5.9 years ago by Charles Warden 8.3k

score 0 · Answer 3 · 2019-02-15

If you're not a fan of using the command line, you could try GenSAS. I saw their presentation at PAG and from what I gather you can carry out gene annotation through their website by just supplying the raw sequencing files. They integrate popular tools, so you can run everything through them.

I'm not sure if this is what you're looking for - your question doesn't state whether you already have the transcriptome etc files and want to use them to annotate a genome sequence, or whether you're looking for these files to help you annotate genes.