【正文】 print ($q_pnu proteins)\n\n。 } printf HIT %s\t%s\t%\n, $arr[0],$arr[1],$pm_score。print_end。 printf Hit%3d: Ortholog pathway for: %20s. With score: %\n\n, $ii,$spec, $total_score{$spec}。big_matrix_sort($aa_db, $q_aa)。 $usage = \n $0 query_pw query_aa protein_db\n query_pw: query pathway file query_aa: query aa file protein_db: protein db to search\n\n。 Part 1. Parse input, check files my ($usage, $q_id, $q_aa, $q_pnu, $q_pw, $aa_db)。 amp。 my ($qid, $i, $j, $ln)。 push (ln3, $hid)。 $hsp_len = abs($end$bg)+1。 print Ref.: US . \Methods for Establishing Pathway Database\n。 while (DB) {if ($_=~/Total keys\s(\d+)/) {$aa_nu=$1。 system (sort k 3rn /tmp/$$.matrix /tmp/$$.)。 my ($bg, $end,$hsp_len,$pm_score)。 $i++) { my (ln1, ln2, ln3, $sc, $hid, $k)。}} close (AA)。 for $file ($q_pw, $q_aa, $aa_db) { if (!(e $file)) { die Did not find $file file\n。 different cells/conditions, different expressions The Need for Pathway Informatics ? Good angle for data integration and representation. ? Research tool for scientists. Learning tool for students. ? Pharmaceutical drug discovery efforts would benefit from prehensive pathway databases and tools. ? A challenge for postgenomic era List of Pathway Databases/Tools Name: KEGG (Kyoto Encyclopedia of Genes and Genomes) Web: Owner: Institute for Chemical Research, Kyoto University Description: KEGG is an effort to puterize current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes and to provide links from the gene catalogs produced by genome sequencing projects. The KEGG project is undertaken in the Bioinformatics Center, Institute for Chemical Research, Kyoto Univ. Name: PathDB Web: Owner: National Center for Genomic Resources Description: PathDB? is a functional prototype research tool for biochemistry and functional genomics. One of the key underlying philosophies of their project is to capture discrete metabolic steps. This allows them to build tools to construct metabolic works de novo from a set of defined steps. PathDB is not simply a data repository but a system around which tools can be created for building, visualizing, and paring metabolic works. List of Pathway Database/Tools (cont.) Name: GenMapp(Gene MicroArray Pathway Profiler) Gladstone Institute, UCSF. GenMAPP is a puter application designed to visualize gene expression data on maps representing biological pathways and groupings of genes. The first release of GenMAPP beta is available with over 50 mouse and human pathways. They also provide hundreds of functional groupings of genes derived from the Gene Ontology Project for the human, mouse, Drosophila, C. elegans, and yeast genomes. GenMAPP seeks collaborators in the biological munity to assist in the development of a library of pathways that will enpass all known genes in the major model anisms. Name: SPAD: Signaling Pathway Database Graduate School of Geic Resources Technology. Kyushu University. There are multiple signal transduction pathways: cascade of information from plasma membrane to nucleus in response to an extracellular stimulus in living anisms. Extracellular signal molecule binds specific intracellular receptor, and initiates the signaling pathway. Now, there is a large amount of information about the signaling pathways which control the gene expression and cellular proliferation. They have developed an integrated database SPAD to understand the overview of signaling transduction. SPAD is divided to four categories based on extracellular signal molecules (Growth factor, Cytokine, and Hormone) that initiate the intracellular signaling pathway. SPAD is piled in order to describe information on interaction between protein and protein, protein and DNA as well as information on sequences of DNA and proteins. Specific Pathway Databases ? Cytokine Signaling Pathway DB. Dept. of Biochemistry. Kumamoto Univ. – The Database contains information on signaling pathways of cytokines. It is designed for researchers who work with cytokines and their receptors, and provides biochemical data and references about signaling molecules as well as ligandreceptor relationships. ? EcoCyc and MetaCyc Stanford Research Institute – EcoCyc database describes the genome and the biochemical machinery of E. coli. The database contains uptodate annotations of all E. coli genes. EcoCyc describes all known pathways of E. coli smallmolecule metabolism. Each pathway and its ponent reactions and enzymes are annotated in rich detail, with extensive references to the biomedical literature. The Pathway Tools software provides query and visualization services. BIND (Biomolecular Interaction Network Database) UBC, Univ. of Toronto BIND is a database designed to store full descriptions of interactions, molecular plexes and pathways, including interactions between any two molecules posed of proteins, nucleic acids and small molecules. Chemical reactions, photochemical activation and conformational changes can also be described. Abstraction is made in such a way