Align sequences without loading subject into RAM

Question

[tucanj]

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!

[John]

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

[tucanj]

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.

Answer 1

[Bara'a]

Try Clustal 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 :)

[tucanj]

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

[Bara'a]

@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 :)

[Bara'a]

Hello there @tucanj :)

This is the reply I got from the Clustal team.

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 :)