i want phylogeny analysis of protein sequences using Neighbour-joining method,i.e. wants neighbours to join in clusters. proteins have different seq length, range 45-434 is there any strategy to extends protein sequence length in comparable manner if i go through regular analysis,is it meaningful that neighbours will joins any software/algorithm who compares diff length of protein seq?
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written
by
Sagar Nikam
2 answers
To address this issue I would rather suggest using T-Coffee since it aligns the protein sequences employing various strategies even considers the structural information resided within the protein. I've found T-Coffee to be much better (than tools such as ClustalW) when the aligned sequence have varied length.
For proteins differing in length, you may want to try Dialign as it does not impose a gap penalty and will find local regions of homology. MEME may also be helpful as it focuses on shared motifs. If you are finding it really difficult to align these sequences, I would suggest SATé, which I have found useful for improving poor alignments.
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Multiple sequence alignment software should accommodate sequences of different length already. I interpret your question like so: which software is best suited for sequences of very different length.