Microbial Genomics & Bioinformatics Group, SKMML, SJTU
Microbial Bioinformatics Group, SKMML, SJTU 
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  Bioinformatics database, tool and web server of interest  
Mobilome analysis (genomic islands)
Bacterial genome annotation, comparative analysis and visualization
Prediction of PKS/NRPS, and metabolic pathway
Mobilome analysis (genomic islands)  
  • Cumulative GC profile, describes the GC content variation along genomic sequences
  • MobilomeFINDER, in silico and experimental discovery of bacterial genomic islands
  • Islander,a database of precisely mapped genomic islands in tRNA and tmRNA genes
  • IslandViewer3, a computational tool that integrates three different genomic island prediction methods
  • IS Finder, reference centre for bacterial insertion sequences
  • PHAST, a fast phage search tool
  • CRISPRFinder, Identification of clustered regularly interspaced short palindromic repeats
  • INTEGRALL, collection of integron sequences and genetic arrangements
  • ACLAME, a classification of Genetic Mobile Elements
  • VFDB, virulence Factor database
  • PAIDB2, pathogenicity island database
  • DrugBank, a knowledgebase for drugs, drug actions and drug targets
  • TTD, therapeutic Target Database
  • ARDB, antibiotic Resistance Genes Database
  • ICEberg, bacterial integrative and conjugative elements database
  • SecReT4, bacterial type IV secretion systems (T4SS)
  • T3DB, bacterial type III secretion systems (T3SS)
  • TADB, type II toxin-antitoxin system, inducing programmed cell death, may regulate the island stability
  • DEG, essential genes in more than 10 bacteria; few of them are found to be carried by genomic islands
  • dndDB, Genomic islands involving into the phosphorothioation of DNA backbone
  • deltarho-web, calculate the dinucleotide distribution bias of GI versus the whole genome
  Bacterial genome annotation, comparative analysis and visualization
  • mGenomeSubtractor, Parallel in silico subtractive hybridization analysis of multiple bacterial genomes
  • WebACT, Database of sequence comparisons between prokaryotic genome sequences
  • Mauve, Multiple Genome Alignment
  • MUMmer, Ultra-fast alignment of large-scale DNA and protein sequences.
  • xBASE, Database for comparative bacterial genomics
  • xBASE Annotation Service, quick annotation for unfinished bacterial genome sequences where a similar reference sequence is available.
  • CGview, generate circular genome maps
  • CGview server, a comparative genomics tool for circular genomes
  • MicrobesOnline, an integrated portal for comparative and functional genomics
  Prediction of PKS/NRPS and metabolic pathway
  • DoBISCUIT, a database of secondary metabolite biosynthetic gene clusters
  • antiSMASH, antibiotics & secondary metabolite analysis shell
  • NRPS-PKS, a knowledge based resource for analysis of Non-ribosomal Peptide Synthetases and Polyketide Synthases
  • SBSPKS, Structure based sequence analysis of polyketide synthases
  • NRPSpredictor, Specificity Prediction of Adenylation domains in NRPS
  • PKS/NRPS Analysis Web-site, HMM implementation for domain parsing and a domain substrate prediction
  • Norine, platform that includes a database of nonribosomal peptides together with analysis tools
  • ClustScan, an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures
  • CLUSEAN, a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters
  • PathPred, An enzyme-catalyzed metabolic pathway prediction server
  • SMURF, genomic mapping of fungal secondary metabolite clusters
  • Pathguide, a collection containing information about biological pathway and molecular interaction related resources


Science Building, Shanghai Jiaotong University, 1954 Huashan Road, Shanghai 200030, China
Created in June, 2006 | 沪交ICP备2010754