Saturday, April 24, 2010

Bioinformatics:Multiple sequence alignment different formats:


Bioinformatics:Multiple sequence alignment different formats:
People sometimes find it confusing when it comes to different multiple sequence alignment formats (what to use with what???), that's because the variety of programs that handles multiple sequence alignments, sometimes you find a program that uses FASTA format and sometimes MSF (Multiple Sequence Format)...etc.

The reason why there are a lot of formats out there, is that every format had appeared by specialists in a specific field, for example specialists in phylogeny use Phylip format...etc

So before you use any format you have to ask yourself questions like: is this format supported by the program i'm running, is it easy for me to modify in it, is it widely accepted...etc.

Some of the most popular multiple sequence alignment formats:

1- FASTA: a text format that's widely accepted and its easy to read and modify.
2- MSF: (Multiple Sequence Format), the most popular, supported by most programs, easy to read and difficult to modify.
3- ALN: produced by ClustalW, easy to read and widely supported.
4- Phylip: text format, supported by most phylogenetic packages.

Any question, u're welcome.


saboo said...

thanks .......

Kinow said...

Hi there! Is there a tool to convert between these formats? Please :)


the-shadow said...

There are actually many conversion tools available on the web. You can just do a Google search and it will return many of them. Here are some of them:

You can choose whatever offers the output formats that you wish. Good luck

kuhan said...

hi, am new for bioinfomatics especially a.a sequencing, So i am self learning it for phd project. Reading a book from arthur lecks. But nothing beats your videos.... now i am playing compared to reading...thank you again.

the-shadow said...

Hi Kuhan, i'm really glad i helped. I myself prefer visual learning, especially live demonstrations. Good luck with your project, and thanks for your comment

harishkumar said...

Thanks dear u make each and every posting awesome.

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