MSA webserver for large datasets ?

Question

[Brett]

I am looking for a webserver that will allow me to perform multiple sequence alignment on approx 10,000 proteins (Muscle/Clustal etc).

Unfortunately due to circumstances beyond my control I cant install anything locally, making this task difficult. Is there any webservers that can handle large data sets such as this? (most seem to be limited to 1000)

Answer 1

[Andreas]

Sounds like a job for Clustal Omega which is designed for such big data-sets. A webserver is available here at the EBI, but they limit the number of input sequences to 2000. You can also try the pasteur webserver but it's likely to have similar restrictions.

Andreas

[Brett]

Many Thanks, in the end I split the data into 5 parts and used Clustal Omega as you suggested (annotating each one afterward).