Question: Multi Sequences Alignment
0
gravatar for Ardmore
7.8 years ago by
Ardmore140
Ardmore140 wrote:

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.

sequence alignment • 2.1k views
ADD COMMENTlink written 7.8 years ago by Ardmore140

proteins or nucleotides?

ADD REPLYlink written 7.8 years ago by Darked894.2k
4
gravatar for Will
7.8 years ago by
Will4.5k
United States
Will4.5k wrote:

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.

ADD COMMENTlink written 7.8 years ago by Will4.5k

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

ADD REPLYlink written 7.8 years ago by Alastair Kerr5.2k

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

ADD REPLYlink written 7.8 years ago by Will4.5k
3
gravatar for Darked89
7.8 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:

There is also fairly new version of t-coffee:

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

ADD COMMENTlink written 7.8 years ago by Darked894.2k
2
gravatar for Alastair Kerr
7.8 years ago by
Alastair Kerr5.2k
The University of Edinburgh, UK
Alastair Kerr5.2k wrote:

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

ADD COMMENTlink written 7.8 years ago by Alastair Kerr5.2k
1
gravatar for Jorge Amigo
7.8 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

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.

ADD COMMENTlink written 7.8 years ago by Jorge Amigo11k

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.

ADD REPLYlink written 7.8 years ago by Alastair Kerr5.2k

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!

ADD REPLYlink written 7.8 years ago by Jorge Amigo11k
1
gravatar for Abdel
7.8 years ago by
Abdel150
Montreal
Abdel150 wrote:

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 .

ADD COMMENTlink written 7.8 years ago by Abdel150

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

ADD REPLYlink written 7.8 years ago by Abdel150
1
gravatar for 2184687-1231-83-
7.8 years ago by
2184687-1231-83-4.9k wrote:

You could also try PRANK: http://www.ebi.ac.uk/goldman-srv/webprank/

ADD COMMENTlink written 7.8 years ago by 2184687-1231-83-4.9k
0
gravatar for Kartik Sunagar
7.8 years ago by
Porto, Portugal
Kartik Sunagar290 wrote:

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.

ADD COMMENTlink written 7.8 years ago by Kartik Sunagar290
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