FASTR3D: 一個快速且準確搜尋相似RNA三級結構的工具

Abstract

FASTR3D是一個架構在網路上的搜尋工具，它允許使用者快速且精確的搜尋PDB資料庫中相似的RNA結構。目前，它允許使用者輸入三種查詢的格式： (i) 一個RNA三級結構的PDB代碼(預設值)，可伴隨一段特定的殘基(residue)範圍， (ii) 一段使用點與括號表示法(dot-bracket notation) 的二級結構，可伴隨輸入其一級序列，與 (iii) 一段FASTA格式的RNA一級序列。另外，使用者也可以指定一些額外的過濾選項來執行FASTR3D： (i) PDB資料庫中RNA結構的發佈日期， (ii) 用來決定RNA結構的實驗方法，與它們最小的解析度(resolution)。FASTR3D是以雜湊表當作搜尋相似RNA結構的核心演算法，來增加搜尋時的速度。我們預先將現有的PDB代碼轉換為二級結構，同時將它們分割成許多不重疊的k-tuples並儲存在一個表格中。然後FASTR3D可利用輸入的二級結構重疊k-tuples去搜尋雜湊表並找出二級結構完全一樣的RNAs。最後，如果查詢的是一個RNA三級結構，FASTR3D會更進一步地透過3D過濾器來過濾掉一些三級結構與輸入結構不相似的RNAs。在輸出的頁面，FASTR3D將會標示出使用者查詢的RNA分子以及使用者設定的選項，接著再顯示出找到結構相似RNA的詳細列表。特別的是，當查詢的RNA是三級結構時，FASTR3D提供一個圖形畫面以顯示出每一個找到RNA的三級結構與輸入結構之間的重疊。FASTR3D目前可以在線上讓使用者使用，其網址在http://bioalgorithm.life.nctu.edu.tw/FASTR3D/。

FASTR3D is a web-based search tool that allows the user to fast and accurately search the PDB database for structurally similar RNAs. Currently, it allows the user to input three types of queries: (i) a PDB code of an RNA tertiary structure (default), optionally with specified residue range, (ii) an RNA secondary structure, optionally with primary sequence, in the dot-bracket notation and (iii) an RNA primary sequence in the FASTA format. In addition, the user can run FASTR3D with specifying additional filtering options: (i) the released date of RNA structures in the PDB database, and (ii) the experimental methods used to determine RNA structures and their least resolutions. FASTR3D uses hash table as kernel algorithm to search for similar RNA structures, and it can make the searching more efficiently. We transform PDB codes into secondary structures, and store them in a table of non-overlapping k-tuples beforehand. Then, FASTR3D can find RNAs whose secondary structures are exactly equal to that of the query by searching overlapping k-tuples of the query secondary structure against the hash tables. Finally, FASTR3D further screens out those RNAs whose tertiary structures are not similar to that of the query by a 3D-filter, if the query is a tertiary structure. In the output page, FASTR3D will show the user-queried RNA molecule, as well as user-specified options, followed by a detailed list of identified structurally similar RNAs. Particularly, when queried with RNA tertiary structures, FASTR3D provides a graphical display to show the structural superposition of the query structure and each of identified structures. FASTR3D is now available online at http://bioalgorithm.life.nctu.edu.tw/FASTR3D/.