| Comparative genomics is an important content in post-genome era. F acing huge and complicated genome data in comparative genomics, developing a suitable genome analysis tool plays key role in raising working efficiency. We designed and developed the "SeqAs" for sequence analysis. It had 20 pieces of module, involving sequence editor, amino acid translating, online Blast alignment and statistics of sequence datasets etc. The analytic function of the software was comparatively comprehensive. It was able to browse and search for multiple sequence alignment and put results of blast into analytic files. After many practical runs, it expressed stable and reliable in various situations. It was also easy to use with friend interface.The genome sequence data were obtained from many plant databases, especially Arabidopsis genome database, the protein database of Swiss-Prot and nucleic acid and protein database and EST database of GeneBank. Combined with reliable gene predicting software FgeneSH, the SeqAs was used to make homology comparative analysis for genes of disease-resistant, metabolism, protein synthesis, cell-growth and cell-division between A rabidopsis and rice genome. The results indicated that 22.6% (54 in 239 Arabidopsis genes) found homology in various degrees in rice (Oryza sativa ssp. Japonica) genome. The homology was relatively low. The order of homology degree in these 5 kinds of genes is protein synthesis, cell growth, metabolism, cell division, some signal transduction, with their homology rate 100%, 80%, 52.2%, 44.4% and 6.9% respectively. There were 14 gene sequences of very high homology (E value 1E-30) on DNA level; 16 sequences of high homology (1E-4E value <1E-10); 16 sequences of low homology (E value >E-4). On the amino acid level, there were 16genes with high homology, 2 sequences of high homology, 7 sequences of lowhomology. Further analyses were made for those sequences of high homology in theirposition, annotation and EST extension.
|
PDF Full Text Request