Question
I am using three different multiple sequence alignment methods which are clustal omega, Mafft, and muscle. On sample of data , the length of generated sequences after alignment was on equal (same length) and on other case generated clustal length size was different than the two others. How Can I assure that the length of variables generated from different MSA should be the same or different?
I applied three multiple sequence alignment methods of muscle, mafft and clistal omega on 30 sequences and 400 sequences . In the case of 30 seq, the output of alignment from the 3 methods was in the same length but in the case of larger data with different length of sequences (input data) the output from alignment methods was different length clustal length is different than the two others. My question is how can i assure that the length from MSA should be equal or different?
- The length of alignment does not matter, and it would depend on the sequences. Just avoid thinking about it.
- Different alignment method will give you different results, all will be correct and no one can say which method is better than other without any details.
- Please get basic/further understanding about MSA, its use/purpose and result usage/interpretation.
I am not comparing the best MSA methods, i just need to know why the input sequences when they are on same length,the output after using different MSA become on equal length but when the input are in different length, the output is in different length
Malik Sallam it is fastaQ sequences, if the input (sequences) on same length, the output after alignment is in equal length but if the input of sequences were in varied length the output of only clustal length is different than Muscle and Mafft.
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