Importance of Synteny in Homology Inference
Ali Zeeshan Ijaz, Raja Hashim Ali, Asima Sarwar, Talha Ali Khan, Muhammad Muneeb Baig
Abstract
Homology inference is central to many Bioinformatics analyses, from phylogeny to evolutionary rates, where the goal is to identify the genes that have evolved from the same last common ancestor. An error at the stage of inferring homology may be carried down to further analysis and may cause severe errors at the later stages. For example, an incorrect pair of genes classified as homologous may lead to incorrectly changing the topology of phylogeny inferred from using the non-homologous pair or incorrect evolutionary rate inference. At the moment, most homology inference algorithms are based purely on similarity in gene contents, which is known to be inversely proportional to the rate of evolution and time since the divergence of both sequences. However, another important characteristic for homology inference is synteny - the order of genes on the homologous chromosomes, which has been rarely used in homology inference. The major reason for not using synteny for homology inference is equal or sometimes drastic affected by the rate of evolution and time since divergence of both sequences. However, using synteny in addition to gene similarity has shown promising results. In the current study, we have tried to explore the usefulness of synteny and present cases, where synteny can aid in differentiating for borderline homologs.