which one is better to do, blastx or blastp?

Question

[seta]

Hi all,

I would like to annotate the transcriptome assembly via homology research. For this purpose, I can do either blastx or blastp. Although blastx is actually finding ORF at 6 frams+blastp and so more time consuming, at the moment I'm confused that which one is better to catch the most informative information and why. Please advise me with your helpful experience.

Best

Answer 1

[Antonio R. Franco]

BlastX requires as query a DNA sequence

BlastP requires as query a protein

If you have a DNA sequence, BlastX will take care of translating your DNA taking into account all of the 6 putative frames, making sense and unsense (read real and unreal) protein sequences. Then, it will go to the protein database to look for homology,and compare all proteins giving you the homologous one. Thus, it will make the selection of the proper protein and frame for you

[seta]

Thanks. I know what you mentioned. My questioned is which one (blastx or blastp) is preferable to get the most informative information and not to miss anything?

[Antonio R. Franco]

What are you starting with ?

Protein or Nucleic acid data ?

If nucleic acid is your data, BlastX will be preferable because it will check for you what is the right frame coding the protein of interest.

If you don't use BlastX starting from nucleic acid data, you have to translate yourself the sequence to a protein, and then run BlastP. This is a harder task for you to accomplish, and also you cannot handle all of the 6 putative frame encoded proteins without having a huge effort and higher chances to miss everything up

If you use protein sequence data, it is not sense to make this question

[seta]

Thanks, as I mentioned in the post, I can do either blastx (using nucleotide sequence) or blastp (protein sequence resulted from nucleotide sequence translation). I have both sequence types and no limitation to do blastx or blastp. Again, my question is if anybody has experience that for example blastx results are more informative than blastp output for the nucleotide sequence and the corresponding protein sequence, respectively?

Answer 2

[Antonio R. Franco]

After BlastX translate the sequence to the correponding protein, it does a BlastP