Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
MegaBLAST vs NUCmer benjaminversteeg Bioinformatics 4 10-28-2014 08:19 AM
How to do a discontinuous MEGABLAST using megablast? maimaiti2008 Bioinformatics 4 08-28-2013 11:07 AM
confused on megablast gigigou Bioinformatics 4 07-30-2013 04:34 PM
Megablast ***** No hits found ****** NGSnoob Bioinformatics 2 08-25-2010 11:34 PM

Thread Tools
Old 02-02-2017, 10:33 AM   #1
Location: US

Join Date: Apr 2010
Posts: 61
Default Megablast x dc-megablast

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?
clarissaboschi is offline   Reply With Quote

blast, megablast

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 07:05 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO