Pattern Of Insertion And Deletion In Mammalian Genome

The completion of the most mammalian genomes,especially the human genome, marking the contemporary biology into the post-genome era .The sequences be measured by Gigabit of so many genomes contains rich an unknown information.,the challenge of the contemporary biologists is to extract and analysis these information. One major aim of genomics research is to identify differences between genomes of species or individuals. The differences of genomes require genetic variation. One mechanism that increases genetic variation is mutation. There are many kinds of mutations. A mutation in which one"letter"of the genetic code is changed to another is a point mutation. Lengths of DNA be deleted or inserted in a gene means a deletion or insertion, respectively.Finally, genes or parts of genes can become inverted or duplicated. Nucleotide substitutions, together with insertions and deletions (indels) are the primary types of mutations which are the major driving forces for genome evolution. Although there are more substitutions than indels, previous researches suggested that indels, instead of substitutions, comprise the majority of the genomic divergence . Therefore, the study of the patterns of insertion and deletion is necessary to understand the mammalian evolution.Sequence alignment is a powerful tool to study the differences between genomes and the evolution of species.The core of sequence alignment is the scoring system,including the scoring matrices and the gap penalties,is mainly derived from the distribution of insertion,deletion and substiturion.The purpose of this study is to obtain a scoring system which have solid evolution basis and base on insertion,deletion and substitution,so as to do a correct sequence alignment.In this research, The multiple alignments of 28 vertebrate species were downloaded from UCSC Genome Bioinformatics website. Olny the multiple alignments of 14 mammalian genomes were used to analyze the patterns of insertions and deletions. We calculated the number and the frequencies of insertions and deletions, Then we studied their length distributions. In this paper, following results were obtained: (1) The single nucleotide insertion and deletion are the most frequent in all events, The percentage of single nucleotide insertions varies from 28.63% to 41.78%, and the percentage of single nucleotide deletions varies from 26.54% to 45.93%.(2)The research of insertions and deletions of gap length no more than 10bp of 14 mammalian genomes show that , Deletions occur more frequently than insertions over all gap lengths.The ratio of deletions to insertions varies from 1.21 to 1.87.However,in opossum,insertions occur more frequently than deletions. The ratio of deletions to insertions is 0.85:1.The data of insertions and deletions used in this study was many times of previous study,howerer the results are basically the same.Therefore, the high percent of single nucleotide insertion and deletion and deletions occur more frequently than insertions seems to be a common phenomenon in the genomic evolution. (3) Both the number of insertions and deletions decrease rapidly with the increases of gap length. (4) Compared with the power low,the probability of insertions and deletions, as a function of gap length, fits the gamma distribution very well.