Multiple sequence alignment

Multiple sequence alignment

• 1.
  Multiple Sequence Alignment
• 2.
   Multiple SequenceAlignment(MSA) is generally the alignment of three or more biological sequence (Protein or Nucleic acid) of similar length.  From the output, homology can be inferred and the evolutionary relationship between the sequence studied.
• 3.
  Dynamic Programming approach Progressivemethod Iterative method
• 4.
   In fact,dynamic programming is applicable to align any number of sequences.  Computes an optimal alignment for a given score function.  Because of its high running time, it is not typically used in practice.
• 6.
   In thismethod, pairwise global alignment is performed for all the possible and these pairs are aligned together on the basis of their similarity.  The most similar sequences are aligned together and thenless related sequences are added to it progressively one-by-one until a complete multiple query set is obtained.  This method is also called hierarchical method or tree method
• 9.
   A methodof performing a series of steps to produce sucessively better approximation to align many sequences step-by-step is called iterative method.  Here the pairwise sequence alignment is totally avoided.  Iterative methods attempt to improve on the weak point of the progressive methods the heavy dependence on the accuracy of the initial pairwise alignment.
• 11.
   Clustal W Clustal W2  Clustal Omega  Kalign  MAFFT  MUSCLE  M View  T-Coffee  Web PRANK  MEME  MACAW
• 12.
   Detecting similaritiesbetween sequences(closely or distinctly related).  Detecting conserved regions or motifs in sequences.  Detecting of structural homologies.  Thus, assisting the improved prediction of secondary and tertiary structures of proteins.