Solving the Challenge of Multiple Alignment with 4000 Sequences

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Discussion Overview

The discussion revolves around the challenge of performing multiple sequence alignment (MSA) with a large dataset of 4000 sequences. Participants explore software options and algorithms suitable for handling such a volume, including ClustalW and alternatives.

Discussion Character

  • Exploratory, Technical explanation, Debate/contested

Main Points Raised

  • One participant inquires about the maximum number of sequences that can be processed by ClustalW, noting issues with both offline and online versions of the software.
  • Another participant suggests using BLAST, although they acknowledge it may not be suitable for MSA, and mention the possibility of writing a custom program for alignment.
  • A different participant clarifies that BLAST is primarily for aligning sequences to a database rather than performing MSA.
  • One participant recommends checking if the university has the GCG software package, which includes multiple programs that might facilitate MSA.

Areas of Agreement / Disagreement

Participants express uncertainty about the best approach to take for MSA with 4000 sequences, with no consensus on a specific software solution or method. Multiple competing views on software options remain unresolved.

Contextual Notes

Limitations include the lack of information on the specific capabilities of ClustalW regarding sequence limits and the potential need for custom programming solutions. The discussion does not resolve the effectiveness of suggested alternatives.

Who May Find This Useful

Researchers or practitioners in bioinformatics, particularly those dealing with large-scale sequence alignment challenges.

karthik3k
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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:
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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? http://www.genetics.wayne.edu/dwomble/gcghelp.html"
 
Last edited by a moderator:
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 don't have enuf time 2 code for similar programs.
 
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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