please share your experience for ORF prediction +blastp instead of doing blastx

Question

[seta]

Hi everybody,

I plan to do ORF prediction followed by blastp instead of doing blastx to annotate my transcriptome assembly generated from a non-model plant. I know there is a lot of ORF prediction tools, preventing to easily choose one of them. I would be highly appreciated if you could please let me know which tool is the better of other in your experience.

Thanks

Answer 1

[lakhujanivijay]

blastp program search protein databases using a protein query. How are you planning blastp with ORFs?

For a comparison of blastp and blastx, you might consider reading from below link http://benzer.rutgers.edu/DSAP/Projects/project2011/Users/Help/BLASTx-vs-BLASTp.pdf

blastx would take longer as the query is translated nucleotide searched against protein databases.

Answer 2

[colindaven]

For a transcript assembly I don't think there are too many alternatives to transdecoder. It is very decent in my experience and will give you the candidate proteins you need to do blastp analysis.

For a genome Maker is very solid providing you think carefully about what ests and proteins to give it as evidence.