Question: Change maximum number of sequences on source code of ClaustalW
0
gravatar for mfonsecarossi
2.1 years ago by
mfonsecarossi0 wrote:

Hey, good evening! I have a very large dataset of protein sequences and would like to know how I change the ClustalW source code to align a larger number of sequences? I saw that I can use the flag "--maxseqlen=n" for change the length of sequences , but I don't known how to change the number of sequences. Someone could help me? Thank you so much Mariana Rossi

alignment • 656 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by mfonsecarossi0

As others have indicated below changing programs is one option but it would only get you so far. If you truly have a gigantic dataset and need to use all of it you may need to find appropriate hardware or trim the dataset down.

ADD REPLYlink written 2.1 years ago by genomax62k

Thank you so much everybody! Mariana

ADD REPLYlink written 2.1 years ago by mfonsecarossi0
0
gravatar for Josh Herr
2.1 years ago by
Josh Herr5.6k
University of Nebraska
Josh Herr5.6k wrote:

I'm pretty sure you can run as much sequence data as possible through ClustalW, not that it has the memory to handle it. I do not see a flag for adjusting the memory of ClustalW. What have you tried? Have you tried to run all your data through ClustalW? You might be confined by your computer memory.

There are other aligners which are more memory efficient, such as MUSCLE, which might better suited for your large dataset of protein sequences.

ADD COMMENTlink written 2.1 years ago by Josh Herr5.6k
0
gravatar for jrj.healey
2.1 years ago by
jrj.healey10k
United Kingdom
jrj.healey10k wrote:

It might be worth considering a different aligner if you're having problems with Clustal instead of rummaging around in its source code.

MUSCLE is pretty good at handling lots of sequences.

ADD COMMENTlink written 2.1 years ago by jrj.healey10k
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