中文摘要

隨著愈來愈多的原核生物基因體被定序完，利用完整序列來探討原核生物間的多樣性也變得可行，許多比較基因體學的研究致力於尋找物種間的相似性與差異性。由於原核生物在形態的辦識困難以及生活環境的多樣性，導致在分類及演化的地位上較難有一致的結論，直到以分子演化的方式才得以分析原核生物間親緣關係，特別是16S rRNA的鑑定將現生生物畫分成三個主要的生命形態。而生活在極端環境下的微生物，如嗜高溫菌、嗜酸菌、嗜鹽菌…等，也有研究指出在核酸及胺基酸組成上有所偏好，更有許多研究利用全基因體的特性來重建原核生物的演化地位。因此，我們建立了一個資料庫- GPDB (Genome Profile DataBase)，目的是提供生物學家利用全基因體的資訊來探討原核生物的演化與多樣性。目前這個資料庫包括了145株 (strain) 完整定序的原核生物，共有223個染色體與質體，含429177條ORFs。原始的序列及物種的分類資料源自於NCBI的GenBank與Toxonomy資料庫，為了能自動化分析這些資訊，我們以perl語言寫了「Genome Profile Pipeline」用來分析不同的genome profiles，包括核酸組成 (GC & AT content, total GC & AT skew, N-nucleotide frequency, codon usage…)、胺基酸組成 (N-peptide frequency distribution), 蛋白體組成 (length & Mw & pI & transmembrane helix protein & fold…)，並以MySQL資料庫作為後端，以圖形化網頁的方式呈現並比較不同生物的genome profiles，並且應用Hierarchical clustering的方式協助類似特徵的歸類，此外，我們也提供虛擬的二維電泳，助蛋白體學上的分析研究。整個網站以模組化的方式設計，以方便日後加入新的genome profiles，提供更多全基因體上的資訊來探討原核生物的多樣性。

Abstract

With rapidly generated whole genome sequence data especially those microbial organisms, it can be used to explore the diversity of ancient life. More and more comparative genomic methods have been used to investigate the similarities or dissimilarities between organisms. Phylogenetic tree based on 16S rRNA indicates the prokaryotic evolutionary relationship unrevealed from the morphological characteristics. Other features like GC content and amino acid composition are widely used to account for extreme environmental organisms such as thermophiles, acidophiles, halophiles, etc. Quarrying the whole genome wide information may suggest why microbe diverse. Here we constructed a database GPDB (Genome Profile DataBase) with 145 microbial genomes including bacteria and archaea. The original sequence data and annotations are based on NCBI GeneBank and RefSeq databases. The uniform nomenclature and classification were used according to the taxonomy database at NCBI. In order to automatically process so many features, the program called "Genome Profile Pipeline" has been developed in perl language. Here we present lots of various "Genome Profile", such as basic information (taxonomy, genome size, orf number…), nucleotide composition (GC & AT content, total GC & AT skew, N-nucleotide frequency, codon usage…), and amino acid composition (N-peptide frequency distribution, proteome distribution like length & Mw & pI & transmembrane helix protein & fold…) in graphic ways. In order to estimate different combination interactively, an on-line graphic browsing interface which use Euclidean distance for hierarchical clustering method was built to compare and view the difference between these organisms. Further more, the website is modulated for more Genome Profile to be included and compared in the future.

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