Multi Sequences Alignment

Question

[Ardmore]

Hi, I have 100 sequences. Each of them has 6000 chars. I want to find a way to align them. Any tools or algorithms?

Thanks.

[Darked89]

proteins or nucleotides?

Answer 1

[Will]

I would suggest MUSCLE which can be downloaded and run on just about any architecture. You'd be hard-pressed to find an online resource which would let you run something that large.

[Alastair Kerr]

muscle used to be good at protein but poor at DNA alignments (compared to clustalw): anything changed?

[Will]

I've never had any problems ... Actually I think it was a Biostar response that suggested I move from ClustalW to Muscle.

Answer 2

[Darked89]

There is also fairly new version of t-coffee:

http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html

Answer 3

[Alastair Kerr]

Have a look at UCLUST but you may also wish to familiarise yourself with authors misgivings on big alignments

Answer 4

[Jorge Amigo]

although this is a very basic and general question, I can't resist answering that a simple search on google for "sequence alignment" will return 2 entries on wikipedia (sequence alignment itself and sequence alignment software) that are of great help for beginners on sequence alignment field.

as a future advice, you don't need to invest your time posting basic questions on an advanced forum, since any search engine will take you to the best places to start reading about what you need.

[Alastair Kerr]

I have not check the memory footprint for a 100 X 6000 alignment in traditional global alignment programs. I look at that and think 'big alignment'... maybe I'm just showing my age.

[Jorge Amigo]

come on Al, don't be so cruel to yourself. sure clustal was a breakout when it first arrived, but if natural selection has ever taught us something is that survival comes through adaptation. examples like MUSCLE (already mentioned here) or MAFFT (my current choice when I need sequence alignments) are great implementations which have enormously reduced memory footprint by rearranging concepts. and I'm sure you have done the same through the years!

Answer 5

[Abdel]

you can use Clustalw , Muscle ..

there is a tool called Geneious which include many alignment algorithms , you can download evaluation version for windows , it is very easy to use .

[Abdel]

http://www.geneious.com/default,28,downloads.sm

Answer 6

[2184687-1231-83-]

You could also try PRANK.

Answer 7

[Kartik Sunagar]

Although I love all the tools mentioned here, I rate MUSCLE as the best and is my personal favourite. If you have a lot of 3D structures available for your gene, you could use PROMALS3D which uses the structural information as well in aligning the sequences which is particularly useful at times.

Don't forget to correct the sequence alignment by eye , as no matter what tool you use you never get a perfect alignment.