Query regarding multiple sequence allignment

[Ashish_Shelar]

I want to allign about 4700 sequences belonging to a domain in a protein. Can someone tell me which tool (online /standalone) can be used to carry out the above task?? thanks

[mfursov]

Do I understand correctly that you need to keep original domain alignment without any changes but align new sequences to it independently?

If this is exactly what you need, please check Unipro UGENE tool and this page:

[Only registered users see links. ]

for "Aligning Sequences to Profile with MUSCLE"

Note that this function is available only with UGENE. Original MUSCLE package allows you align profile-2-profile only.

[Ashish_Shelar]

Dear mfursov.. I have downloaded sequences belonging to a particular domain only and i intend to allign them.MUSCLE allows alignment of upto 500 sequences only. So i cant use it . any other suggestions?

[mfursov]

Why do you think that MUSCLE is limited by 500 sequences only? Is this error reproducible with your data only?

[verginov - metalife.com]

Your choice is very good. According to the authors of the algorithm, Muscle is able to align 5000 sequences of average length 350 in 7 min. Some alternative programs are T-cofee and ClustalW. The ClustalW tool is slower, but has more adjustable options.