Hi,
I have more than 4000 files containing orthologous gene clusters in each file from a bacterial community. How can I perform multiple sequence alignment of all the files in fast and efficient manner? Should I use clustal W, if yes how?
Thanks!
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utkarsh.sood •
Thanks for your help! Do I have to upload 4000 files separately (as each file contain multiple sequence for 1 protein) ?
If you need to align each file separately yes, If you want to align them all at the same time you can concat them all in one file. for example; you can run this command in the directory that contains all files
cat `ls *.fasta` > files_concat.fasta
also you can download it and use it locally
If you need really fast alignment, I suggest you to try mafft (http://mafft.cbrc.jp/alignment/software/), it has some really fast and accurate methods for that. But if your files are small you can use clustalw / clustal omega / muscle / t_coffee or whatever you want.
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As long as the individual files are not large you may be able to use any MSA program. Basically you are looking to do 4000 separate MSA's? A cluster would be the way to go for something this large.
This paper discusses acceleration of MSA's but requires special hardware which you may not have.
I have the access to server with 24 cores and 128Gb RAM.Can I create multiple ClustalW alignments for thousands of fasta in a directory. The input would be: 1.fasta, 2.fasta... 6405.fasta; where a given file commonly contains14 or more proteins.
The output would be:1.aln, 2.aln... 6405.aln