I want to cluster a set of sequences whose conservation level are not very high despite of highly conserved sequences locally. Could anyone help me with it? Thanks!
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I would suggest an all vs. all blast
then use a clustering algorithm like mcl, http://micans.org/mcl/
by playing with the inflation value you can control the clustering.
Ciaran
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savetherhino.org
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The immune system’s power comes from its genetic diversity, allowing myriad threats to be neutralized through first recognizing foreign antigens. That diversity is also what makes the immune system so difficult to study. Recent advances in sequencing technology and computational biology, however, are giving researchers new tools to understand immune responses and immune-related diseases in greater detail.
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