MEGABLAST Search

MegaBlast implements a greedy algorithm for the DNA sequence gapped alignment search. Since MegaBlast can only work with DNA sequences, the only program it supports is Blastn. For user convenience, the MegaBlast page supports both MegaBlast and regular blastn search. MegaBlast currently does not support the graphical overview of the alignments, so this option is automatically turned off when the MegaBlast checkbox is checked.

Input

MegaBlast takes as input a set of FASTA formatted DNA query sequences. These can be either pasted into a provided text area, or downloaded from a file. It is preferrable to submit many query sequences at a time, but not more than 16383. The algorithm concatenates all the query sequences together and performs search on thus obtained long single sequence. After the search is done, the results are re-sorted by query sequence.
The database input for MegaBlast is any "blastable" database, obtained from the ftp server or via formatdb program from a FASTA formatted file.

Gapping parameters

Unlike BLAST, MegaBlast is most efficient in both speed and memory requirements with non-affine gap penalties, i.e. gap opening cost of 0 and gap extension penalty E = match_reward/2 - mismatch_penalty. These values of gapping parameters are default. To set the affine penalties, advanced options should be used. It is not recommended to use the affine version of MegaBlast with large databases or very long query sequences.

Advanced Options

-W Word size.

Any value of W, that is not divisible by 4, is equivalent to the nearest value divisible by 4 (with 4i+2 equivalent to 4i). When W is divisible by 4, MegaBlast finds any exact match of length W that starts at a position in the database sequence divisible by 4 (count starting from 0). Thus it is guaranteed that all perfect matches of length W + 3 will be found and extended by the MegaBlast search. It is preferrable to use MegaBlast with word sizes at least 12. With word size 8 the algorithm becomes much slower. All other advanced options have the same meaning as in regular BLAST.