|
171-bp SUBSEQUENCE CONVERGENCE-DIVERGENCE DIAGRAM |
||||
|
Author: Matko Gluncic (matko@phy.hr)
|
||||
|
If you use 171-bp SUBSEQUENCE CONVERGENCE-DIVERGENCE DIAGRAM as a tool in your published research, we ask that the
following reference be cited: Rosandic, M., Paar, V., Gluncic, M., Basar, I., Pavin, N. |
||||
|
Each monomer copy within a given genomic sequence diverges from other monomer copies in that sequence by 20-40 %, except for alpha monomers within HORs. Each alpha monomer in one HOR copy differs from the corresponding alpha monomer in the other HOR copy by less than 1%: the first monomers in all HOR copies are convergent to each other, the second monomers in all HOR copies are convergent to each other, ...(except for those having large insertions or deletions). Exploiting this feature, we have devised the following novel graphical method to identify HORs in a given genomic sequence. First step. An array of 171-bp subsequencesis formed: subsequence No. 1 - from position 1 to 171 in genomic sequence; subsequence No. 2 - from position 2 to 172 in genomic sequence; subsequence No. 3 - from position 3 to 173 in genomic sequence; and thus all the way to the end of the given genomic sequence. Second step. We compute divergence of the No. 1 subsequence with all 171-bp subsequences from the set. Then we assign to No. 1 the pairs of numbers (k,l) = (1,l) where l is No of those subsequences that diverge from the No.1 subsequence less than 3%. We repeat a same procedure for all 171-bp subsequences. Third step. Every pair of numbers from the second step is displayed graphically: the first number of the pair is taken as coordinate on the horizontal axis and the second as coordinate on the vertical axis. Outside of the HOR domain we obtain the points on a single monotonically increasing line, while in the HOR domain we obtain a series of parallel lines due to convergence between every n-th monomer. Some irregularities in the pattern of parallel lines reflect larger insertions and deletions in the HOR sequence. |
||||
|