Question: MegaBLAST vs NUCmer
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gravatar for a.b.versteeg
6.2 years ago by
a.b.versteeg0 wrote:

Hi,

For a project I'm trying to find out which aligner is best for aligning whole bacterial genomes.

Important aspects for choosing the best aligner are speed and sensitivity. In this situationĀ NUCmer and BLAST seem both great programs for making the local alignments. To find out which suits best, I've ran some tests. I found out that

  • MegaBLAST is a bit more sensitive than NUCmer, because it finds more alignments, but also breaks off alignments more quickly.
  • At the aspect of speed NUCmer is BLASTed away with a factor of 3 to 4. Both programs are very fast though.

My question remains, what advantages would one have when using NUCmer instead of BLAST?

Thank you

blast alignment genome • 1.9k views
ADD COMMENTlink written 6.2 years ago by a.b.versteeg0

beyond just the algorithm there is the scoring scheme that affects your alignments,

by default megablast has a zero penalty for gap start and a large penalty for gap extension, you can modify these as well.

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Istvan Albert ♦♦ 86k
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