Maximal path based conflict resolution approach in multiple homologous gene list alignment

This paper deals with the alignment of multiple homologous gene lists, which is a specific problem of multiple sequence alignment. In this case, the smallest unit of the input sequences is comprised of complete genes. An efficient graph based algorithm for the alignment of multiple homologous gene lists is presented in this paper. The fundamental concept to multiple sequence alignment and the graphical structure of the genomic segments are provided. Two heuristics are developed for the resolution of local alignment conflicts which reduces the search space while searching for the candidate link for deletion. The performance of the proposed algorithm is assessed by comparing the alignment results of homologous genomic segments in Arabidopsis thaliana to those obtained by using other alignment methods.