Align very big .fasta files

[miguelangel]

Hi!

I need to align big fasta files in any way. I have tried to align them in some web-servers, but my files are too big to be run in there.

I have also tried to align them with some freeware, but they are not able to run such an amount of data.

I need to do this with bacterial 16S, fungal ITS and algal rbcL data.

I will be very glad if you could help me.

Thanks a lot.

[maubp]

Have you tied BLAT (the BLAST-Like Alignment Tool)?

http://en.wikipedia.org/wiki/BLAT_%28bioinformatics%29

[miguelangel]

Thanks maubp, but if I am not wrong, BLAT is useful if you work with short/shotgun sequences. It would be also useful for 454 sequences?

I am trying to get started with it, anyway.

Thanks again.

[maubp]

Sorry, I misunderstood you - when you said big FASTA files I (wrongly) assumed you mean large genomes. BLAT is good for that, but neither it nor BLAST is so good for lots and lots of small sequences like next generation sequencing reads.

If you are dealing with 454 sequences you should look into read alignment tools, the Roche 'Newbler' gsMapper is a sensible choice.

[miguelangel]

Thanks a lot.

I am going to look about gsMapper right now.