Align Multikb Contigs Of A Mammalian Genome Against List Of Mammalian Genome Assemblies

Question

[Ahdf-Lell-Kocks]

I would like to be able to align multi-Kb contigs of a non-assembled mammalian genome against the list of available mammalian genomic assemblies. I would like to do this locally since I have got many query sequences but I am not going to align the whole of the sequences of this genome, since I am doing this on a targeted manner. How can I do these alignments?

I thought I would concatenate all mammalian assemblies labeling the sequence regions with the species name and put them all into one big multi-fasta file. Then index it with bwa 0.6.1 and query this index file with bwasw.

Any other suggestions? Blast+? Blat?

Answer 1

[Neilfws]

Another suggestion: MUMmer.

[ALchEmiXt]

+1 for MUMmer who can do the job of query vs multiple genome FASTA in one run.

Answer 2

[Niallhaslam]

It sounds like the kind of job clustal omega was designed for:

http://www.clustal.org/omega/

[ALchEmiXt]

Not familiar with omega but isn't it just scaled to handle quickly many many many SHORTer sequences? That's mostly the issues with existing multiple aligners... the sequences tend to be too long.