Question: An Alternative To Blastx With Speed Similar To Bowtie
4
gravatar for Tianyang Li
7.2 years ago by
Tianyang Li490
Beijing, China
Tianyang Li490 wrote:

Hi,

Is there any fast aligner that aligns nucleotide sequences to protein databases?

I've used blastx but blastx is too slow and takes too much memory, I'm wondering if anything like bowtie exists.

Thanks!

ADD COMMENTlink modified 6 months ago by h.mon24k • written 7.2 years ago by Tianyang Li490
3
gravatar for Martin A Hansen
7.2 years ago by
Martin A Hansen3.0k
Denmark
Martin A Hansen3.0k wrote:

Maybe Usearch might be useful.

ADD COMMENTlink written 7.2 years ago by Martin A Hansen3.0k
2
gravatar for Neilfws
7.2 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

You could try BLAT (downloads) with the options:

-t=prot -q=dnax

I've only used it for nucleotide-nucleotide searches, but it should be faster than BLAST. You just need sufficient RAM for the in-memory database indices.

ADD COMMENTlink written 7.2 years ago by Neilfws48k

Apparently blat can't do this. I got this when I ran it: d and q must both be either protein or dna

ADD REPLYlink written 7.2 years ago by Tianyang Li490

Really? Interesting, I've never tried and just assumed it had a blastx-like function.

ADD REPLYlink written 7.2 years ago by Neilfws48k

A new answer brought me back to this old thread.

The error message "d and q must both be either protein or dna" is not correct; it should begin "t and q". Furthermore, this error occurs when -q=dna, not -q=dnax as I suggested. The error in the latter case is "Unrecognized combination of target and query types."

An answer in this thread suggests simply switching the -t and -q options (i.e. -q=prot -t=dnax).

ADD REPLYlink modified 5.1 years ago • written 5.1 years ago by Neilfws48k

Blat with options -t=prot -q=dnax gives results similar to tBLASTn but not BLASTx. Be careful during the comparisons.

ADD REPLYlink written 5.1 years ago by Prakki Rama2.2k
2
gravatar for Dgg32
5.1 years ago by
Dgg3260
Bremen
Dgg3260 wrote:

RAPsearch 2 can do DNA vs protein or protein vs protein, very fast.

ADD COMMENTlink written 5.1 years ago by Dgg3260
1
gravatar for Len Trigg
4.0 years ago by
Len Trigg1.2k
New Zealand
Len Trigg1.2k wrote:

The mapx command from Real Time Genomics is for this specific scenario. As well as being inherently very fast, it also supports multiple cores. It is included in our commercial RTG Metagenomics and RTG Core products, as well as the non-commercial version of RTG Core.

 

ADD COMMENTlink written 4.0 years ago by Len Trigg1.2k
1
gravatar for h.mon
6 months ago by
h.mon24k
Brazil
h.mon24k wrote:

I know I am reviving a really old thread, but it is surprising no one has cited DIAMOND so far. It is not particularly light on resources, but it is incredibly fast.

ADD COMMENTlink written 6 months ago by h.mon24k

All true, but unfortunately it stinks at doing blastX-like searches

ADD REPLYlink written 6 months ago by lieven.sterck4.5k

really? besides protein-protein searches, I understood this was one of the principal objectives of the algorithm. What do you mean?

ADD REPLYlink written 6 months ago by Carambakaracho970
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