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1、与细菌有关的生物数据库,/nar/database/a/,毒力基因鉴定 噬菌体及前噬菌体 分泌系统 细菌基因组注释 细菌基因组比对 细菌宿主相互作用 rRNA,毒力基因鉴定,Isfinder,A database of bacterial Insertion Sequences http:/www-is.biotoul.fr,Islander,Pathogenicity islands and prophages in bacterial genomes /islander,VFDB - Viru

2、lence Factors Database,Reference database for microbial virulence factors ,Comparison of pathogenomic composition of Streptococcus,HGT-DB, Horizontal Gene Transfer-DataBase,Putative horizontally-transferred genes in prokaryotic genomes http:/www.fut.es/debb/HGT/,噬菌体和前噬菌体,PHAST (PHAge Search Tool), P

3、HASTis a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as we

4、ll as phage “cornerstone” feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence

5、 data and Genbank files, provide richly annotated tables on prophage features and prophage “quality” and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and line

6、ar genomic views.Furthermore, tests indicate that PHAST is as accurate or slightly more accurate than all available phage finding tools, with sensitivity of 85.4% and positive predictive value of 94.2%.,Example,1: NC_009442 Streptococcus suis 05ZYH33, complete genome Length: 2,096,309 nt 2: NC_01292

7、5 Streptococcus suis P1/7, complete genome Length: 2,007,491 nt 3:NC_009443 Streptococcus suis 98HAH33, complete genome Length: 2,095,698 nt,phiSITE,Gene regulation in bacteriophages ,分泌系统,ABCdb,Archaeal and bacterial ABC transporters http:/www-abcdb.biotoul.fr,Effective,Predict

8、ed secreted bacterial proteins Bacterial protein secretion is the key virulence mechanism of symbiotic and pathogenic bacteria. Thereby effector proteins are transported from the bacterial cytosol into the extracellular medium or directly into the eukaryotic host cell. The Ef

9、fective portal provides precalculated predictions on bacterial effectors in all publicly available pathogenic and symbiontic genomes as well as the possibility for the user to predict effectors in own protein sequence data.,TADB,Type II Toxin-Antitoxin loci in bacteria and archaea http:/bioinfo-,细菌基

10、因组注释,BacMap,Picture atlas of annotated bacterial genomes http:/wishart.biology.ualberta.ca/BacMap,DEG - Database of Essential Genes,Database of essential genes from bacteria and yeast ,FusionDB,Database of bacterial and archaeal gene fusion events http:/igs-rs-mrs.fr/FusionDB/,GeneDB,Curated databas

11、e for protozoan and bacterial genomes sequenced at the Sanger Centre /,NMPDR - National Microbial Pathogen Data Resource,A database for functional annotation and comparative analysis of microbial genomes ,PEC - Profiling of E. coli Chromosome,Comprehensive data

12、base on E. coli genome http:/shigen.lab.nig.ac.jp/ecoli/pec,PGTdb - Prokaryotic Growth Temperature database,Prokaryotic growth temperature database .tw,ShiBase,Comparative genomics of Shigella ,细菌基因组比对和分析,TIGR Comprehensive Microbial Resource,Completed microbial genomes http:

13、//tigr-scripts/CMR2/CMRHomePage.spl,Colibri,E. coli genome database at Institut Pasteur http:/genolist.pasteur.fr/Colibri/,EMGlib - Enhanced Microbial Genomes Library,Completely-sequenced prokaryotic genomes http:/pbil.univ-lyon1.fr/emglib/emglib.html,ERGO-Light,Integrated biochemical da

14、ta on 10 bacterial genomes: Publicly-available portion of the ERGO database http:/www.ergo-,GenoBase,E. coli genome database at Nara Institute http:/ecoli.aist-nara.ac.jp/,GenProtEC,Escherichia coli K-12 genome, gene products, and homologs ,LEGER,Comparative genomics of pathog

15、enic and non-pathogenic Listeria spp. http:/leger2.gbf.de/cgi-bin/expLeger.pl,MtbRegList,Gene expression in Mycobacterium tuberculosis http:/www.USherbrooke.ca/vers/MtbRegList,SuperCAT,A database for multilocus sequence typing analysis of the Bacillus cereus group of bacteria http:/mlstoslo.uio.no/,

16、SubtiList,Bacillus subtilis 168 genome http:/genolist.pasteur.fr/SubtiList/,细菌及蛋白相互作用,hp-DPI,Database of protein interactions in Helicobacter pylori .tw/hp/,操纵子分析,DOOR,Predicted operons in bacterial and archaeal genomes /OperonDB/,OperonDB,Predicted operons i

17、n bacterial and archaeal genomes /cgi-bin/operons/help.cgi,ODB - Operon database,Operon database http:/www.genome.sk.ritsumei.ac.jp/odb/,蛋白功能预测,OMPdb,Beta-barrel outer membrane proteins from Gram-negative bacteria http:/bioinformatics.biol.uoa.gr/OMPdb,PSORTdb,Protein subcellul

18、ar localization in bacteria /,HEG-DB,Predicted highly expressed genes in prokaryotic genomes http:/genomes.urv.cat/HEG-DB,COG - Clusters of Orthologous Groups of proteins,Protein families from complete microbial genomes /COG,2D-PAGE,Proteome database syste

19、m for microbial research http:/www.mpiib-berlin.mpg.de/2D-PAGE,NRSub,Bacillus subtilis genome http:/pbil.univ-lyon1.fr/nrsub/nrsub.html,P2CS,Prokaryotic 2-Component Systems P2CS is an integrated and comprehensive database of two-component system (TCS) signal transduction proteins,

20、 which contains a compilation of the TCS genes within completely sequenced genomes and metagenomes. It provides detailed annotation of each TCS gene including sequence features, functional domains, as well as chromosomal localization. Data can be downloaded for analysis and users can validate and ad

21、d annotation to predicted TCS genes.,rRNA,RIDOM - Ribosomal Differentiation of Medical Microorganisms,rRNA (16S and ITS) sequence-based identification of medical microorganisms http:/www.ridom.de/,RISSC - Ribosomal Internal Spacer Sequence Collection,Ribosomal 16S-23S RNA gene spacer regions http:/e

22、gg.umh.es/rissc,RRNDB,Variation in prokaryotic ribosomal RNA operons /rrndb/index.php,PromEC,E. coli mRNA promoters with experimentally identified transcriptional start sites http:/margalit.huji.ac.il/promec/,RegulonDB,E. coli transcriptional regulation and operon organization http:/regulondb.ccg.unam.mx/,谢 谢,EcoCyc,E. coli K-12 genome, metabolic pathways, transporters, and gene regulation networks. /,SILVA: a comprehensive online

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