what is the best to use, blast x or blast n?
I have results from KEGG and I want to do Blast for some genes in NCBI, Do you think Blastx better or Blastn??I just want to know if these genes are complete genes or no and also i want to know if it is reported or not?? please help me as i want to do that as soon as possible???
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walaa.shaalan •
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You may have to do both (your post is thin on details). Start with
blastnand then useblastxif needed.so it is no difference between the to uses? I know that Blastx get hits with amino acids and Blastn get hits with nucleotides. I mean the main idea or the main result is the same or not?
Both are doing sequence searches so only in that sense there is no difference.
What is going to be different are the results since the databases you are going to be searching against will be different. If you are not able to identify a sequence by plain
blastnsearch you may need to move on to other methods.See this recent post it may help:
Why there is a big difference for blastn and blastx results of a given sequence
From my experience, they give different numbers of hits.