help
Posted: Sun Jan 15, 2006 4:53 pm
how do i use clustal-w 
ClustalW is a way to align sequences using an algorithm. There are a few different formats - some web-based others that you can download and run without the internet. I usually use the web-based one at EMBL-Ebi
http://www.ebi.ac.uk/clustalw/
There is a FAQ that you should read before running the program. It explains what you can do with ClustalW and how to change the settings to do specific things.
To begin with leave all of the settings boxes at the default ( "def" or whatever they are set to). Just paste in your sequences into the box marked "Enter of paste a set of sequences in any supported format". The format i usually use is called FASTA. If you get your sequences from a database, like Genbank, you can select to view or download the sequences in FASTA. Basically it is all of the letter of the sequence preceeded by a ">" sign and the name of the sequence. Do not put lots of space between your sequences.
The output will show you the sequences aligned next to each other and give you a measure of how many residues are identical, how many similar and so on. These are also marked on the sequence.
Good luck with your alignments,
-Caroline