Question: please share your experience for ORF prediction +blastp instead of doing blastx
0
gravatar for seta
3.6 years ago by
seta1.1k
Sweden
seta1.1k wrote:

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

ADD COMMENTlink modified 2.4 years ago by colindaven1.2k • written 3.6 years ago by seta1.1k
0
gravatar for Vijay Lakhujani
2.4 years ago by
Vijay Lakhujani4.0k
India
Vijay Lakhujani4.0k wrote:

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.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Vijay Lakhujani4.0k
0
gravatar for colindaven
2.4 years ago by
colindaven1.2k
Hannover Medical School
colindaven1.2k wrote:

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.

ADD COMMENTlink written 2.4 years ago by colindaven1.2k
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