mRNA to protein

Question

[Xylanaser]

Hey

1. How can I translate mRNA (fasta) to protein? I mean i have transcriptome. I want to turn it to proteome. Is there any tools for that? Biopython?
2. Is method of choosing longest ORF of RNA good?

Please give me advice/ your opinion.

Cheers

[lieven.sterck]

yes, looking for the longest ORF is the most common thing to do. This will likely report a fair number of false positives as you will find an ORF on nearly all 'transcripts'

Alternatively, but more work, is to indeed run some ORF finding/predicting tool on it, eg: TransDecoder, FrameD, ... Will result in less false positives

[Xylanaser]

thanks ;) found https://www.ncbi.nlm.nih.gov/orffinder/

[pld]

https://github.com/TransDecoder/TransDecoder/wiki

Answer 1

[GenoMax]

EMBOSS is always a good source for these types of tools. transeq (for translation, http://emboss.sourceforge.net/apps/cvs/emboss/apps/transeq.html ) and getorf (http://emboss.sourceforge.net/apps/cvs/emboss/apps/getorf.html ) are relevant tools.

There are web based version available if you want to use them that way.

Answer 2

[Elisabeth Gasteiger]

For a simple interactive tool, you may also try ExPASy's Translate tool (https://web.expasy.org/translate) - there is a new beta version available right now, waiting for feedback.

Answer 3

[h.mon]

As lieven.sterck said, protein prediction tools will have less false positive than just longest orfs. TransDecoder is a good tool, but it is tightly integrated with Trinity so it may complain a bit, or may not output all the info possible, if your transcriptome is from other source. FrameDP, in my experience, is less sensitive than TransDecoder.

Another good option is GeneMarkS-T (free for academic use only).