生物资讯研究所暑期学分班指南.pdfVIP

生物資訊研究所暑期學分班 生物資訊技術: Linux系統管理實務 Linux 生物資訊工具實務 (二) 蛋白質結構預測與交互作用 2006/08/15 Ying-Hsueh Huang 1 事前準備 1.下載 Putty 以及登入遠端主機 20 2.下載 PDF 格式的講義 .tw/~sakula/ 2006/08/15 Ying-Hsueh Huang 2 Primary structure analysis Secondary structure prediction Tertiary structure 2006/08/15 Ying-Hsueh Huang 3 Primary structure analysis Primary structure refers to the linear sequence of amino acids Pattern and profile searches Pfam HMM search ─ scans a sequence against the Pfam protein families db PROSITE scan ─ Scans a sequence against PROSITE RPS-BLAST is the search tool used in the CD-Search service InterPro Scan ─ integrated search in PROSITE, Pfam, PRINTS and other family and domain databases 2006/08/15 Ying-Hsueh Huang 4 Pfam – Protein families database of alignments and HMMs http://www.sanger.ac.uk/Software/Pfam/ 2006/08/15 Ying-Hsueh Huang 5 It is a database of protein domain families. It contains curated multiple sequence alignments for each family and corresponding hidden Markov models (HMMs) (Eddy S.R., 1998). Profile hidden Markov models are statistical models of the primary structure consensus of a sequence family. The construction and use of Pfam is tightly tied to the HMMER software package. 2006/08/15 Ying-Hsueh Huang 6 Pfam: Databases 2 databases: Pfam-A – curated multiple alignments. – Grows slowly. – Quality controlled by experts. Pfam-B –automatic clustering (ProDom derived). – Complements Pfam-A.