Blast-like program to use with MEGAN?

[kga1978]

Hi All,

I need to run some analyses on large datasets that I will be analysing in MEGAN. I need to run BLASTX and BLASTN (like) searches, but both programs are very very slow and I constantly run into programs with not allocating enough memory. Does anybody know of other programs I could use instead of BLAST? I have been looking into the following:

LAST
USEARCH
FR-HIT
RapSearch

Overall I think they should all be faster than blast, but they also come with various problems - some of them don't output blast-format and others don't control memory very well (e.g. I need to blast against the nr database with 2gigs of ram). Any ideas or suggestions? I'm leaning towards LAST as I can control memory quite well, but I'm not sure how fast it is and it also doesn't directly output to blast format.

I welcome any suggestions - thanks.

[tujchl]

you can try LAST (http://last.cbrc.jp/), which is very similar with blast. The speed of LAST is comparable with bowtie

[cliffbeall]

Usearch

I can confirm Usearch is faster than BLASTx, with a trade-off in sensitivity.

For some tests I did a few months ago it varied depending on the parameters, the most sensitive Usearch was 12.5X faster at 93% of the BLASTx sensitivity (sensitivity defined as no. of query hits with the test data I was using).

The output format was not directly compatible with MEGAN, that would require some massaging to get working. If you come up with a script that works, I'm sure folks would appreciate if you shared.

[jrvalverde]

Try BLAT. We are testing it right now and comparing results with BLAST.