BioInfo-> MSA

[karthik3k]

How do i do a Multiple Alignment with 4000 sequences.
offline version of ClustalW hangs

online version accepts only 500 sequences
What is the maximum number of sequences that can be given to CluatalW ???
Any other gud softw .
PLease let me know ...

[Monique]

4000 sequences? :eek: I don't know, but couldn't you use BLAST or something? I know you can write a program which allows you to automatically have all your sequences aligned, but it might not really be the type of algorythm you want to use.

Have you heard of GCG sequence analysis? GCG (http://www.genetics.wayne.edu/dwomble/gcghelp.html)

[karthik3k]

BLAST ???
No Monique.
BLAST-Basic Local ALignment Search Tool
its only for aligning a given sequences to a Db(Set of sequences).
I donno any other program for MSA and i dont have enuf time 2 code for similar programs.

[Monique]

As I said, it might not be the algorythm for you. I seriously would find out if your university has the GCG software package, there are many programs included in it and I'm pretty sure you'll be able to do multiple alignments with one of them.