When I should use discontinuous Megablast instead of Megablast? I do not know which blast is better to use for nucleotide blast.
I read some information about it as follow:
Megablast: Retrieves highly similar sequences and is very fast. It efficiently find long alignments between very similar sequences -- it is intended for comparing a query to closely related sequences and works best if the target percent identity is 95% or more. The MegaBLAST program is useful for extremely rapid scans of a nucleotide database with a large batch of nucleotide queries, such as EST sequences.
Discontiguous megablast: for more dissimilar sequences, should be used for cross-species comparisons, allows for some mismatches. Retrieves more dissimilar sequences than megablast, but is more sensitive than blastn. It uses an initial seed that ignores some bases (allowing mismatches) and is intended for cross-species comparisons.
So the main difference is - megablast is better for same species search and dc-megablast is better to search to other species? Anything else?
I read some information about it as follow:
Megablast: Retrieves highly similar sequences and is very fast. It efficiently find long alignments between very similar sequences -- it is intended for comparing a query to closely related sequences and works best if the target percent identity is 95% or more. The MegaBLAST program is useful for extremely rapid scans of a nucleotide database with a large batch of nucleotide queries, such as EST sequences.
Discontiguous megablast: for more dissimilar sequences, should be used for cross-species comparisons, allows for some mismatches. Retrieves more dissimilar sequences than megablast, but is more sensitive than blastn. It uses an initial seed that ignores some bases (allowing mismatches) and is intended for cross-species comparisons.
So the main difference is - megablast is better for same species search and dc-megablast is better to search to other species? Anything else?