Question: Align sequences without loading subject into RAM
1
gravatar for tucanj
15 months ago by
tucanj60
Canada
tucanj60 wrote:

Are there any tools for global alignment where the entire db is not loaded into ram? Blast is the only one I could find but it is too slow. I am looking to align RNA-seq reads to NCBI nt (~70gb) and I do not have that kind of ram.

Thanks!

blast alignment • 407 views
ADD COMMENTlink modified 15 months ago by Bara'a210 • written 15 months ago by tucanj60

Where are you getting a 70Gb transcriptome from? o_O Unless you want to map to multiple species...?

ADD REPLYlink written 15 months ago by John11k
1

Want to do metatranscriptomic analysis by mapping to NCBI nt. I don't want to use DIAMOND as part of MEGAN because I have ncRNA as well.

ADD REPLYlink written 15 months ago by tucanj60
0
gravatar for Bara'a
15 months ago by
Bara'a210
Amman - Jordan
Bara'a210 wrote:

Try Clustal Omega : http://www.clustal.org/omega/

I'm not sure about the way it loads dbs into RAMs, but it provides some pretty good features for global alignment tasks.

It might work for you to run it locally for sequences larger than 2000 or 2MB size by dividing the db into several seperate jobs against your set of RNA reads.

Good luck :)

ADD COMMENTlink modified 15 months ago • written 15 months ago by Bara'a210

My understanding was that Clustal Omega was for aligning sequences against each other and not pairwise to a reference database. Is that correct?

ADD REPLYlink written 15 months ago by tucanj60

@tucanj ... you might be right, I'm not sure if there's any workaround in Clustal Omega command line regarding this  .
I will check that for you :)

ADD REPLYlink written 14 months ago by Bara'a210

Hello there @tucanj :)

This is the reply I got from the Clustal team.

Clustal Team Reply Regarding Aligning RNA-reads to NCBI nt

Apparently, what you were asking for is possible using Clustal Omega BUT NOT for RNA-reads unfortunately.

Hope that helps you one day in some other cases.

Good Luck :)

ADD REPLYlink written 14 months ago by Bara'a210
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