WHAT IS ALIGNMENT?

Alignment

“It is the comparison of  two or more DNA or protein sequence by searching for a series of individual character or character pattern.”

1) Pairwise sequence alignment:-

          a)Local Alignment:-

·       The alignment stop at the end of region of strong similarly and much high similarity is given to finding this local region.

·       It consider only match region.

·       Dashes in the sequence indicate sequence is not included in the alignment.

·       Vertical bar indicate identical region in the sequence.

·       Highest matching called seed.

·       Smith waterman Algorithm is used in this alignment.

e.g. BLAST(Basic local Alignment search tool.)

a)   Global Alignment:-

·       In a global alignment attempt is made to align the entire sequence using all sequence character upto both ends of each sequence.

·       It is consider match, mismatch and gap region also.

·       Sequence that are quite similar and approximately the same length are  suitable candidate is for global alignment.

·       Needleman wunsch Algorithm is used in this alignment.

e.g.FASTA

Principle method for pairwise sequence alignment:-

                                       a) Dot Matrix

                                        b) Dynamic Programming algorithm

a)   Dot Matrix:

This method displays any possible sequence alignment as diagonal on the matrix.Dot matrix analysis can readily reveal the presence of interaction, Deletion and direct and indirect repeat that are more difficult to find out by the other method .This method was first described by Gibbs and McIntyre (1970).

Features of Dot matrix:

The Dot matrix should be visible on Computer terminal thus providing an interactive environment so that different types of analysis.

Use of colour dots can enhances the detection of region of similarity.

Methods of Dot Matrix:-

1)In a Dot Matrix method for sequence comparison one sequence A is listed across the top of the page and the other sequence B is listed down the side.

2) Starting with the first character B the comparison then move across the page in the first raw and places a dot in any column ,where the character in A is the same.

3) The second character in B is then compared to the entire A sequence and the dot is placed in row two wherever the match occurs.

4)This process is continued until the page is filled with dots representing all the possible matches of A character with B character.

5)Detection of matching region may be include by filtering out random matches in the Dot matrix.

6)A large window size is generally used for DNA sequence than for protein sequence, because of the number of random matches expected between unrelated sequence is much greater due to the  use of only 4 DNA symbol as compared to 20amino acid symbols.

                    Sequence A: AGCTAGGA

                    Sequence B: CACTAGGC

7) To maximize the number of matches the resulting alignment could be:-

                          —AGCTAGGA—

                           CA—CTAGG—C

   b) Dynamic Programming algorithm:-

   1)It is a method of sequence alignment ,that can take gaps into account but required a manageable number of comparison.

2)DNA is an efficient recursive method to search thought all the possible alignment and find the one with an optimal score.

3)DNA usually consists of the following three component .

               i)Recursion relation

              ii)Tabular computation                     

              iii)Traceback

4)Needleman and Wunsch first introduced a dynamic programming algorithm for comparing two sequence in 1970.

                                                                                                                  

                                                                                                                       --Shweta Adsule