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云之南

风声,雨声,读书声,声声入耳;家事,国事,天下事,事事关心

 
 
 

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专业背景:计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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生物信息学在线分析工具之其他  

2010-01-05 19:33:56|  分类: 生信分析软件 |  标签: |举报 |字号 订阅

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  • Genetic
    • HaploBlockFinderCincinnati(USA)
    • IMpRH Web ServerINRA
    • LIAN (tests the null hypothesis of linkage equilibrium for multilocus data)Max-Planck(Germany)
    • Linkage Web serversRockfeller(USA)
    • MAP-O-MAT (marker-based linkage mapping server)Rutgers(USA)
    • QGE gSCANHutchinson(USA)

  • ABS (QL prediction, MUSEQAL, Clustal, GOR4, FoReSST)NIH(USA)
  • Alignment Tools (Simmat, Malgen, Malig, Lova)LSI(Spain)
  • Automated analysis
  • All-IN-ONE SEQ-ANALYZER (Homology Search, Protein Analysis, DNA Analysis)Michigan(USA)
  • ASTRAL (Compendium for Sequence and Structure Analysis)Stanford(USA)
  • Barton Group WWW Server (Amas, Scanps, Amps, Assp, Jpred, ProEST, 3Dee)Dundee(UK)
  • BCM Search Launcher (Baylor)BCMentry point(searches, alignments, patterns (Blast, BlastPat, Pima , Beauty, Blitz, Fasta, FastPat, ClustalW, MAP), prediction ...), What'sNew, see alsoBatch Clientfor BCM Search Launcher (Unix, Mac)
  • BiBiServ Sequence Analysis DepartmentBielefeld(DCA, GeneFisher, RIFLE, ROSE, Splits tree) (Germany)
  • Bioinformatics Center (PredictProtein, Meta, PredictNLS, Eva, DSSCont, NORSp)Columbia(USA)
  • Bioinformatics resources (DigiNorthern, KaryoReader, DNA helical stability)Buffalo(USA)
  • Biocomputing Tools (FT, SecStr, Pred-TMR, Pred-TMR2, OrienTM, CoPreTHI, Pred-Class, LSQR, SCAR)Athens(Greece)
  • BioInformatics & Molecular Analysis SectionBIMAS(HLA Binding Prediction, Promoter Scan, Signal Scan, GCG-Lite)
  • Bioinformatics and Pattern DiscoveryIBM(Pattern Discovery, Multiple Sequence Alignment, Homology Search) (USA)
  • BioInformatics ressourcesUMMS(Restriction, TFScan, ORF, Primer, Signal sequence cleavage, Garnier, PRINTS, Blast)
  • Bioinformatics Services at IFOM (Blast, HMMER, GenScan, Assembly, EST Machine, SMS, SeWeR, JaMBW)Rome(Italia)
  • Bioinformatics Toolkit (Blast, Fasta, Clustalw, PredictProtein, SEWER interface)CMBI(Netherlands)
  • Bioinformatics Tools (Meta-Server, P-Sea, TITO, Modeller, SMD, W-Loop, 3D-Evaluation, LEA, SCWRL 2.8)Montpellier(French)
  • Bioinformatics Tools (Emboss, Blast, Phylip ...)Hong Kong
  • Bioinformatics Web (Protein and DNA analysis, EMBOSS, Phylogeny)Indiana(USA)
  • BioI@Sista (Maran, AQBC, Intergenic select, MotifSampler, MotifScanner, Go4G, Toucan)Leuven(Belgium)
  • Biological computing (Sequence analysis, Genomics, Proteomics)Weizmann(Israel)
  • Biological programs accessible through the Web server ofPasteur(France)
  • Biomolecular Modelling Laboratory (Sawted, 3D-PSSM, Prof, Domains, 3D-JIGSAW, Domain Fishing)BMM(UK)
  • BioWWW (Codontree, Patscan, UTRscan, Wordup, Markov)Bari(Italy)
  • BLASTULA (the server of Blast servers)GIFTS(France)
  • The Brutlag Bioinformatics group (emotif, identify, scan, decypher, alion)Stanford(USA)
  • Calculations (Sequence utilities, Trnaslation, rare codons, PCR, Spectro, Bacteria growth, ..) atMolBiol(Russian)
  • CBC protein analysis (PANAL)CBC(Prosite, Blocks, Prints, Pfam) (USA)
  • Computational Biochemistry Research ToolsETH(Darwin, AllAll, AllAllDB, MassSearch, MultAlign, NuclPepSearch, PepPepSearch, TreeGen)
  • Computational BiologyIBM Research(USA)
  • Computational Biosciences Tools (GenQuest, Grail, PROSPECT, Pipeline, Domain Parser, Mira)Oak Ridge(USA), anotherlink
  • Computational Services developed and offered byEMBL(ASC, ClusProt, OBSTRUCT, PredictProtein, PROPSEARCH, SSCP, SSPRED, STRIDE, TMAP), see also "Argos service", see also Comparative Sequence AnalysisBork's group(Heidelberg)
  • Computer Programs (RGSites scan, Predicting activities of functional sites in DNA/RNA, CRASP, CRAFT)MBS(Russian)
  • CSE on line software (EULER, GRIMM, MGR)UCSD(USA)
  • DDBJ Search and analysis (Blast, Fasta, Ssearch, Clustalw, Libra)DDBJ(Japan)
  • DeCypher server (Blast, ClustalW, Framesearch, HMM Framesearch, HMM, Profile, Smith-Waterman)Stanford(USA)
  • Dragon Genome Explorer (Promoter finder, CG+ PF, ATG finder, CpGIslands, Splice sites, PolyA)BRUS
  • Easy (Blast, Fasta, Pfam, Prints, Prosite, Profiles, Blocks)Manchester(UK)
  • EBI servicesEBI(Database, Query, Similarity ...), other servicesEBI(Dali, Bic, Bic_SW, Blast, Fasta3, Clustalw, GeneMark, Ppsearch, Prat, Restrict, SAPS), embosstools
  • Expasytools menu, see also Swiss-Model: Automated Protein ModellingServer
  • Expression ProfilerEBI(UK)
  • Fasta Programs (Fasta, Lalign, Plalign, PRSS, Hydrppathy, Garnier)Virginia(USA)
  • Free on line access (ElDorado, Chip2Promoter, PromoterInspector, MatInspector, SMARTest, DiAlign)Genomatix
  • GeneBee servicesMoscou
  • Genestream (Blast, Fasta, Align, LFasta, LAlign, SSearch, Map ...),IGHM, see alsoIGHM(France)
  • Genetics Programs (Transmit, Phase, Phamily, Haploxt, Genoform, Haploform)Oxford(UK)
  • Genomic analysis Web ToolsSanger(UK)
  • HIV Sequence Database toolsLANL(USA)
  • HMM Applications (Compare, Query, Tune Up : hidden Markov model)UCSC(USA)
  • HNB (Family, function, structure)Berlin(Germany)
  • Honig Lab's Software Server (DelPhi, Surfv, Decoy, Side Chain, Loop, Structure Alignment,..)Columbia(USA)
  • IBM Bioinformatics Groups (Protein annotation, MSA, Pattern discovery, Gene identification...)IBM
  • Integrated Analysis Services (with registration)HGMP(BLAST, NIX, GLUE, PIE, RHyME, MAGI)
  • ISREC Software Homepage (Lausanne)ISREC(BOXSHADE 3.0, Coils, EPFL-BLAST, PatternFind, ProfileScan, PrositeScan, SAPS, TMPred)
  • ISU server (AAT, GeneSequer, SplicePredictor, MyGV, Diverge, MuSeq Box, Alignment,..)Iowa(USA)
  • Jade development environment and demosMontpellier(France)
  • Java-based Molecular Biology Work BenchToldo(Alignment Editor, Pattern Searching, PCR, pI, Oligo, Map, Translate, ..), see alsoBBS(Australia)
  • LBNL Human Genome Informatics GroupLBNL(Gene, promoter, splice sites prediction : (HMM and NN methods))
  • Logiciels au LCB (ESTA, FSED, Recsta)LCB(French)
  • Logiciels pour la biologie (Blast, Clustalw, HMMER, Phylip, Emboss Package, IPPRE, Clustering)CBiB(French)
  • Mass Spectrometry FacilityUCSF(MS-Fit, Tag, Edman, Digest, Product, Comp), see alsoProteinProspector
  • META PredictProtein server (SignalP, NetOglyc, NetPicoRNA, ChloroP, JPred, TmHMM, ToPred, DAS, FRSVR, SAMT98, Swiss-Model, CPHmodels)Columbia(USA)
  • Meta-Server (Pcons2, 3DSHOT3, Blast PDB-Blast, ORFeus, FFAS, 3D-PSSM, GenTHREADER, mGenTHREADER, INBGU, Sam-T99, FUGUE, 123D+, SUPERFAMILY)BLBII(Poland)
  • MMTSB (Multiscale Modeling Tools in Structural Biology)SRI(USA)
  • Modelling server (Vriend's Group : WHAT_IF, DSSP, Check, Secondary structure...)CMBI, see also WHAT IFWeb interface
  • NCBI (PubMed, Entrez, BLAST, BankIt, OMIM, Taxonomy, Structure)NCBI(USA), see alsoDatabases and Tools
  • NCSA BIOLOGY WORKBENCHNCSA(Database Search, Blast, MSA)
  • NetMulPBIL(online multivariate analysis system)
  • NIMR Tools (Quest, Humanisation, Mview, Praline, Repro, Tune1D, Pops, Sap, Psap)NIMR(UK)
  • NPS@ (Network Protein Sequence @nalysis)PBIL(France)
  • On-line Resources From UMBER (Align, Bioactivity, Cinema, Easy, FingerPRINTScan, PRINTS)Manchester(UK)
  • Online Services of the Institute of Enzymology (Hmmtop, Scpred, Scide, Das-Tmfilter, CysRedox, Das)Budapest(Hungaria)
  • PAPIA (Protein structure similarity, Homology, Alignment, TFSEARCH)RWCP(Japan)
  • PIR Integrated Environment for Sequence Analysis (IESA)Georgetown(USA)
  • PIR Searching Databases (Blast, Pattern, Alignment, GeneFind)Georgetown(USA)
  • Plant databases and tools (Motif Sampler, Cluster analysis, SPADS)Plant systems Biology(Belgium)
  • Prediction servers (CPHmodels, HMMgene, NetGene, NetOglyc, NetPicoRNA, NetPlantGene, NetStart, SignalP)CBS(Denmark)
  • Predictor (B2tmpred, Cornet, Cyspred, Dcon, Irene, MaxSubSeq, Ispred, Rcnpred, Secpred, Spep)Bologna(Italy)
  • PRODRG (Vriend's Group : a small molecule interpretation system ; GROMOS, WHATIF, MOL2, MOLDES)Dundee(UK) (PDB format)
  • Programs for Comparison and Recognition of Protein Structures (123D, SARF2, PDP)NCI-FCRDC(USA)
  • Protein Folding and Design Group (Agadir, CHEY, SH3, ADA2h, Helical, Beta)Heidelberg(Allemagne)
  • Protein Prospector (MS-Fit, MS-Tag, MS-Seq, MS-Pattern, MS-Digest, MS-Product, etc.)UCSF(USA), see alsoMelbourne(Australia)
  • Protein Structural Analysis (Secondary structure, Folding, PimaII, Threading)BMERC(USA)
  • Protein Structure Prediction (Casp1, Casp2, Casp3, SOV, ACE)LLNL(USA), see alsoProtInfo
  • PROWLRockfeller(MassBank, MassRef, Protein identification ..), see alsoressources
  • PSCAN (Aligning 2 sequences, finding a match in the database)Stockholm(Sweden), see alsoservices
  • PSIPred server (PSIPred, MEMSAT, GenTHREADER)Londres(UK)
  • Public WWW services (EMBOSS, PHD, Prosite, Phylip, Clustalw, Phylodendron, HTH,..)EMBNet(Spain)
  • RDP-II Online Analyses (Probe, Align, Distance, Chimera, T-RFLP, SubTrees..)CME(USA)
  • SAGE (Serial Analysis of Gene Expression)NCBI, see alsoSagenet
  • Samuel Karlin Group Web Server (SplicePredictor, ITERALIGN, SSPA, GENSCAN)Stanford(USA)
  • SBNet (Structural Biology Network : BioSEL, ProSAL, HetSEL)Uppsala(Sweden)
  • SDSC Biology (WorkBench, Meme, Meta-Meme, Molecular Information Agent, Family Pairwise Search, Conformational Likeness Search, Combinatorial Extension)San Diego(USA)
  • Sequence Analysis & Tools at Stanford (USA)
    • (Blast, Fasta, Primer, PatMatch, Restriction, SAGE, Similarity View..)S. cerevisiae
    • (Blast, Fasta, Primer, PatMatch, Restriction..)Arabidopsis(TAIR)
  • Sequence Analysis Server (Finding genes, Pairwise alignment, Multiple alignment)Michigan(USA)
  • The Sequence Manipulation Suite (DNA entry, manipulation, figures, analysis - Protein entry, manipulation, figures, analysis)Bioinformatics
  • Sequence Tools (Sequence Conversion, Multiple Alignement)TAGC(French)
  • Services (Blast, Smith-Waterman, WuBlast, PFScan, Coils, TmPred, Saps, ...) atEMBNet
  • Services (Pattern, LFasta, LAlign, Align, Fasta, Blast, Blast2, Clustalw, Traduction)InfoBioGenin french (France)
  • Services at the BUM (TFC, UTR, CDS finder, Contig, Clustalw, Fpat, LWA, SENSEI)Michigan(USA)
  • Services (Gene finder, Genome search, Promoter, Protein structure, Protein location) atSoftberry(USA)
  • Services at TOFU (Blast, ScorePeptides, ReadSeq, FmtSeq, Coils2, SeqSearch, Primer3, ClustalW, BoxShade)Texas(USA)
  • Services BiophysWWW supplies (DotPlot, Poland, Tinocco, Langmuir, Construct)Dusseldorf(Germany)
  • SEWER (Blast, Blocks, Cap, Clustal, GeneMark, Primer, Protein Machine, ProtParam, PsiPred, ScanProsite, Webcutter)Bioinformatics, see alsoBari
  • Similarity Search EnginesProWeb(USA)
  • Software at EMBnetNorway
  • Software at EMBnetch.EMBnet
  • Software at the Roth Lab (GoFish, ClusterJudge, Pnet, ChIPper, FuncAssociate)Harvard(USA)
  • Structural Bioinformatics Group (Pints, InterPreTS, Proust, Coiled-coil)EMBL(Germany)
  • Structural Biology on line (Fugue, TraceSuite II, Coda, Petra, Joy, Comparer)Cambridge(UK)
  • Structure Prediction sever (Crystal, Fold, Moment, Errat, Verify3D, Alignment, ..)UCLA-DOE(USA)
  • SWBIC (Pcappss, Blast filter, GraphAlign, Transform, SeqCheck, SeqMake, EnVirusSat)NMSU(USA)
  • TBI services (ZZIP, Blast, Fasta, PRIDE, SYSTERS Cluster...)DKFZ(Germany)
  • TigemNet Sequence Utilities (Blast, UniBlast, EST assembly, CAP, CompBlast, CompFasta, DPS)TigemNet(Italie)
  • Tools for data mining (Blast, COGs, LocusLink, UniGene, ORF finder, Electronic PCR, VAST, CCAP, VecScreen)NCBI(USA)
  • TOPS (Protein Topology : search, compare, cartoon..)EBI(UK)
  • TRADAT (TRAnscription Databases and Analysis Tools)MI(Italy)
  • TRANSFAC (Blast, MatInspector, FastM, PatSearch, SaGa, S-comp, Clustalw, Boxshade, FunSiteP)GBF(Germany)
  • USC Computational BiologyUSC(Alignment, Chimera, Gene Recognition, Procrustes)
  • USF WWW services (SPASM, DEJAVU, HIC-Up, MOLEMAN, MAPMAN, EDS)Uppsala(Sweden)
  • Virtual Genome Center (Alces)VGC(Coding region, Dotplots, Dst, Oligo Tm, Primer, Zinfo)
  • Web-based analysis (Primer, Promoter Scan, Lalign, Pscan, PatmatMotif, STSSearch)Oxford(UK), see also (Phylip, Emboss, Hmmer, Sam packages)WB-Analysis
  • WebGene ServerITBA(Italy) (Gene prediction, Splice, Poly A, Tata Box, MSA, CpG, Repeat, EST)
  • wEMBOSSIBBM(Argentina), see alsoPBI(Canada), see alsoEBI(UK), see alsoOUBC(UK)
  • Workbench (web-based tool for biologists)SDSC(USA)
  • WWW Query (COA, PCO, Recsta, Lfasta, Pattern...)Lyon(France)
  • Yeast Regulatory Tools (upstream region analysis, pattern, orf, oligo, ..)ULB(Belgium), see alsoLCB(Mexico)
  • Zhang Lab server (Gene-finding, Promoter, Poly-A, ESEfinder)CSHL(USA)
  • Index
    • Analysis toolsPasteur(France)
    • DNASYSTEM (Sequence Analysis Site)San Diego(USA)
    • The DEAMBULUM (Optimized Maze in Molecular Biology)InfoBioGen(France)
    • Online Analysis ToolsOntario(Canada)
    • Similarity Search EnginesProweb(USA)
    • Software Seekgenamics(USA)

  • BOXSHADE Pretty Printing and Shading of Multiple-Alignment filesEMBNet, see alosPasteur(France)
  • Buffers for pH controlManchester(UK)
  • CHROMA (tool for generating annotated multiple sequence alignments)Oxford(UK)
  • CNplot (Visualization of Large scale Clustered Networks)Stanford(USA)
  • Drawseq - biosequence drawing toolIndiana(USA)
  • Filtersites (Filter conserved sites in an alignment)Pasteur(French)
  • Fmtseq (sequence conversion)Pasteur(France)
  • GB2xml (Genbank to XML conversion tool)Pasteur
  • JOY (protein sequence-structure representation and analysis)Cambridge(UK)
  • MaxBench (Sequence comparison methods evaluated)Sanger(UK)
  • ModelMaker (to construct mRNA sequences from genomic data)NCBI(USA)
  • MuSeqBox (Multi-query Sequence Blast output examination)ISU(USA)
  • Lowercase low-complexity regions (PSEG)Virginia(USA)
  • PTree (PRINTS Tree)Manchester(UK)
  • The Protein ColourerEBI(by default, colour aminoacids according to their hydrophobicity : settings change available)
  • PrettyPlot MulSeqsUMMS(USA)
  • Reformat sequencesWisconsin(USA)
  • RHIMS (Relative Homology Index using Mathematical Summation) visualisation of Database searchesDundee(UK)
  • Sequence Shuffle (shuffle the order of characters to produce a randomized sequence with the same overall composition)Arizona(USA), anotherlink
  • SHUFFLESEQ (shuffles a set of sequences maintaining composition)Pasteur(France)
  • Tools for alignmentsHeidelberg

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