Dot matrix
- 1. Definition of sequence alignment • Sequence alignment is the procedure of comparing two (pair‐wise alignment) or more multiple sequences by searching for a series of individual characters or patterns that are in the same order in the sequences. • There are two types of alignment: local and global. In global alignment, an attempt is made to align the entire sequence. If two sequences have approximately the same length and are quite similar, they are suitable for the global alignment. • Local alignment concentrates on finding stretches of sequences with high level of matches.
- 2. Methods of sequence alignment • Dot matrix analysis • The dynamic programming (DP) algorithm • Word or k‐tuple methods
- 3. Dot matrix analysis • A dot matrix analysis is a method for comparing two sequences to look for possible alignment (Gibbs and McIntyre 1970) • One sequence (A) is listed across the top of the matrix and the other (B) is listed down the left side • Starting from the first character in B, one moves across the page keeping in the first row and placing a dot in many column where the character in A is the same • The process is continued until all possible comparisons between A and B are made • Any region of similarity is revealed by a diagonal row of dots • Isolated dots not on diagonal represent random matches
- 4. Dot matrix analysis • Detection of matching regions can be improved by filtering out random matches and this can be achieved by using a sliding window • It means that instead of comparing a single sequence position more positions is compared at the same time and dot is printed only if a certain minimal number of matches occur • Dot matrix analysis can also be used to find direct and inverted repeats within the sequences
- 7. Interpretation of dot matrices • Regions of similarity appear as diagonal runs of dots • Reverse diagonals (perpendicular to diagonal) indicate inversions • Reverse diagonals crossing diagonals (Xs) indicate palindromes
- 9. Interpretation of dot matrices • Can link or "join" separate diagonals to form alignment with "gaps" – Each a.a. or base can only be used once • Can't trace vertically or horizontally • Can't double back – A gap is introduced by each vertical or horizontal skip
- 14. Filtering to remove “noise” • A problem with dot matrices for long sequences is that they can be very noisy due to lots of insignificant matches (i.e., one A) • Solution use a window and a threshold – compare character by character within a window (have to choose window size) – require certain fraction of matches within window in order to display it with a “dot”
- 17. How do we choose a window size? • Window size changes with goal of analysis – size of average exon – size of average protein structural element – size of gene promoter – size of enzyme active site
- 18. How do we choose a threshold value? • Threshold based on statistics – using shuffled actual sequence • find average (m) and s.d. (σ) of match scores of shuffled sequence • convert original (unshuffled) scores (x) to Z scores – Z = (x ‐ m)/σ • use threshold Z of of 3 to 6 – using analysis of other sets of sequences • provides “objective” standard of significance
- 19. ADVANTAGES • Fairly easy to Implement. • Easy to understand visually. • Good overview of places fot good alignment. • It shows all possible alignment of pairs. • It can be used in combination of other methods. • Readily reveals the presence of insertions/deletions and direct and inverted repeats that are more difficult to find by the other, more automated methods
- 21. Protein DataBank • The Protein Data Bank (PDB) is a repository for the 3‐D structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X‐ray crystallography or NMR spectroscopy and submitted by biologists andbiochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, andRCSB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. • The PDB is a key resource in areas of structural biology, such as structural genomics