Align very big .fasta files

miguelangel · 11-30-2012, 05:20 AM

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 · 11-30-2012, 06:31 AM

Have you tied BLAT (the BLAST-Like Alignment Tool)?
http://en.wikipedia.org/wiki/BLAT_%28bioinformatics%29

miguelangel · 12-03-2012, 02:10 AM

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 · 12-03-2012, 02:51 AM

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 · 12-03-2012, 03:06 AM

Thanks a lot.

I am going to look about gsMapper right now.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Does BWA cannot align reads to fasta with RYWSM?	dkrtndhkd	Bioinformatics	2	08-05-2012 04:14 AM
How to align diploid ab1 files to the reference genome?	ymc	Bioinformatics	2	06-29-2012 08:38 PM
perl woes and the processing with big fatq files	Kcornelius	Bioinformatics	7	04-19-2012 05:37 AM
Doubt about .abi files and .fasta files	fc35802	Bioinformatics	2	02-28-2012 11:05 AM
Align multiple sequences in tabular or fasta format	pchiang	Bioinformatics	7	07-01-2011 11:18 PM

11-30-2012, 05:20 AM	#1
miguelangel Member Location: Madrid Join Date: Jun 2012 Posts: 16	Align very big .fasta files 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.

11-30-2012, 06:31 AM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Have you tied BLAT (the BLAST-Like Alignment Tool)? http://en.wikipedia.org/wiki/BLAT_%28bioinformatics%29

12-03-2012, 02:10 AM	#3
miguelangel Member Location: Madrid Join Date: Jun 2012 Posts: 16	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.

12-03-2012, 02:51 AM	#4
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	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.

12-03-2012, 03:06 AM	#5
miguelangel Member Location: Madrid Join Date: Jun 2012 Posts: 16	Thanks a lot. I am going to look about gsMapper right now.