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BioInfo-> MSA

  1. Apr 23, 2004 #1
    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 ...
     
    Last edited: Apr 23, 2004
  2. jcsd
  3. Apr 23, 2004 #2

    Monique

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    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
     
  4. Apr 23, 2004 #3
    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.
     
  5. Apr 23, 2004 #4

    Monique

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    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.
     
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