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Figure 1 | BMC Bioinformatics

Figure 1

From: Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice

Figure 1

A modified Smith-Waterman algorithm to locate colinearity. (A) A simplified gene homology matrix (GHM, denoted as H). Genes A1, A2, ..., A18 on chromosome A are arranged horizontally, and genes B1, B2, ..., B14 on chromosome B are arranged vertically. Each cell of the matrix is filled with "1" or "0" based on the homology information from BLASTP search, e.g., gene A1 and gene B1 are homologous, and gene A2 and B2 are non-homologous. (B) A modified dynamic programming procedure. A scoring matrix S is constructed recursively based on H, with mg set to 2 genes apart. The distance criterion demands that neighboring genes in colinearity are no more than 2 genes apart. Pointers are shown by dark or grey arrow lines. Two collinear paths containing 9 and 5 genes are shown by dark arrow lines reflecting the same colinear relationship between the corresponding chromosomal regions.

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BMC Bioinformatics

ISSN: 1471-2105

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