Solving the Challenge of Multiple Alignment with 4000 Sequences

AI Thread Summary
To perform a multiple sequence alignment (MSA) with 4000 sequences, users encounter limitations with ClustalW, as the offline version may hang and the online version only accepts up to 500 sequences. Alternatives to ClustalW are suggested, including the GCG sequence analysis software package, which contains various tools for MSA. While BLAST is mentioned, it is clarified that it is not suitable for MSA as it is designed for aligning sequences to a database rather than performing multiple alignments. Users are encouraged to explore available software options at their institutions to find a suitable solution for aligning a large number of sequences.
karthik3k
Messages
149
Reaction score
0
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:
Biology news on Phys.org
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.
 

Thread 'Flesh-eating New World Screwworm re-occurrence in US'

Deadly cattle screwworm parasite found in US patient. What to know. https://www.usatoday.com/story/news/health/2025/08/25/new-world-screwworm-human-case/85813010007/ Exclusive: U.S. confirms nation's first travel-associated human screwworm case connected to Central American outbreak https://www.reuters.com/business/environment/us-confirms-nations-first-travel-associated-human-screwworm-case-connected-2025-08-25/...
View full post »

Thread 'Chagas disease now established in US'

Chagas disease, long considered only a threat abroad, is established in California and the Southern U.S. According to articles in the Los Angeles Times, "Chagas disease, long considered only a threat abroad, is established in California and the Southern U.S.", and "Kissing bugs bring deadly disease to California". LA Times requires a subscription. Related article -...
View full post »

Thread 'I need help understanding this quote about recent Natural Selection'

I am reading Nicholas Wade's book A Troublesome Inheritance. Please let's not make this thread a critique about the merits or demerits of the book. This thread is my attempt to understanding the evidence that Natural Selection in the human genome was recent and regional. On Page 103 of A Troublesome Inheritance, Wade writes the following: "The regional nature of selection was first made evident in a genomewide scan undertaken by Jonathan Pritchard, a population geneticist at the...
View full post »

Similar threads

Biological Info: Understanding & Analyzing
Replies
15
Views
3K
Automotive Alignment Theory - DIY Help
Replies
20
Views
4K
Challenge Math Challenge - October 2021
2
Replies
61
Views
11K
Challenge Math Challenge - October 2020
Replies
33
Views
8K
Challenge Math Challenge - November 2021
Replies
42
Views
10K
B How can hyperreal numbers make infinitesimals logically sound in calculus?
Replies
24
Views
6K
Challenge Math Challenge - February 2021
2
Replies
67
Views
11K
Challenge Math Challenge - May 2021
3
Replies
114
Views
10K
Challenge Math Challenge - March 2020 (Part II)
2
Replies
51
Views
10K
Challenge Math Challenge - September 2021
3
Replies
100
Views
11K

Hot Threads

Recent Insights

Back
Top