生物学在线工具汇总

sharebio发表于 2011-12-28 8:44:45 856人阅读|2

找生物分享有趣、使用生物资源,分享下不知哪位牛人整理的常用生物软件,罗列如下(均为在线工具),很是方便。

Search a sequence database

  • Sequence comparison
  • BLAST (results with links Databases : D, Entrez : E, Related Sequences : R, SRS : S, Prosite : P)
  • NCBI [E]
    Databases : NR, Month, SwissProt, Dbest, DBSTS, PDB, Vector, Kabat, Mito, Alu, EpD, Yeast
  • ProtEST -Protein matches for ESTs (BLASTX with -e 1e-6) NCBI
  • BCM Proteins, nucleic acids [D, E, R, S]
  • Expasy : blast at NCBI [D] with extra : analyse and align all HSPs
  • IBB (Padoue)
  • IGHM (French) [D]
    Databases : NR, Month, SwissProt, Dbest, DBSTS, GBxxx, PDB, Vector, Kabat, NRSub, Transfac …
  • Strasbourg (Ballast : explore the depths of Blast searches) (French)
  • TBI (Germany) [E, P]
  • Toulouse (French)
  • Organism-Specific Blast NCBI, another link
  • Search of Anopheles gambiae NCBI (USA)
  • Search of Aspergillus nidulans Oklahoma (USA)
  • Search of Complete Genomes (E.C, S.C, M.J, M.G, B.S) BMERC (Blastp, Blastx) (USA)
  • Search of CDD (Conserved Domain Database : rpsblast) NCBI (USA), see also Toulouse (French)
  • Search of Dictyostelium (blastn) : Tsukuba (Japan), see also Jena
  • Search of Drosophila : BDGP (Berkeley) [E]
  • Search of EST (Human, Drosophila, Mouse, EMBLEsT..) EMBL (Germany)
  • Search of E. Coli : Pasteur (French)
  • Search of E. Coli : Birmingham (UK)
  • Search of ESTHER (cholinesterase) INRA (French)
  • Search of Fugu NCBI (USA)
  • Search of HIV-1 (subtyping) NCBI (USA)
  • Search of Human Sanger (UK), see also NCBI (USA)
  • Search of Human MIPS (blastn), see alos cDNA, see also EST (Germany)
  • Search of Human UCSC (USA) (BLAT, not Blast)
  • Search of Human Repeat Oklahoma (USA)
  • Search of “Kegg genome” Kyoto (Japan)
  • Search of Immunoglobulins NCBI (USA)
  • Search of microbial genomes NCBI (USA)
  • Multiple Custom Databases (P.falciparum, P.vivax, P.berghei, P. chabaudi, EST) NCBI (USA)
  • Search of Neisseria gonorrhoeae Oklahoma (USA)
  • Search of P450, UGT, cytochrome b5 Biobase (Denmark)
  • Search of Plant knockout databases SDSC (USA)
  • Search of P. falciparum NCBI
  • Search of protein Databank PBIL (French) [S]
  • Search of Streptococcus pyogenes Oklahoma (USA)
  • Search of UTR Bari (Italy)
  • Search of Zebra fish NCBI (USA)
  • Species-Specific Protein Sequence Searches BCM (USA)
  • PRINTS Blast Manchester (UK)
  • Search of SBASE8.0 Database ICGEB (Italy)
  • BEAUTY and BEAUTYX at BCM (BLAST Enhanced Alignment Utility : options CRSeq, CROS, Domain) ADN, Proteins (info) [D, E, R, S] et alignment for each “cluster”
  • With Entrez and SRS Links BCM [D, E, R, S]
  • Search of NRL_3D PBIL (French) [S]
  • Search of Ex-NRL-3D (SWISS-MODEL Blast) Expasy
  • Search of Ribosomal RNA (SSU, LSU) Gent (Belgium)
  • Gapped BLAST (résultats avec liens Banques : D, Entrez : E, Related Sequences : R, SRS : S, Prosite : P)
  • MEGABLAST : Nucleotide (résultats avec liens Banques : D, Entrez : E, Related Sequences : R, SRS : S, Prosite : P)
  • PHI(Pattern Hit Initiated)-BLAST (résultats avec liens Banques : D, Entrez : E, Related Sequences : R, SRS : S)
  • PSI(Postion Specific Iterated)-BLAST (résultats avec liens Banques : D, Entrez : E, Related Sequences : R, SRS : S)
  • CMBI D
  • NCBI [E]
  • Pasteur [D]
  • Toulouse [D]
  • Search of NRL_3D or SwissProt PBIL (French) [S]
  • Search of microorganisms U-ParisSud (French)
  • Search of protein Databank PBIL (French) [S]
  • SAWTED (Structure Assignment With Text Description) BMM (UK)
  • BLAST2 or WU-BLAST2 (results with links Databases : D, Entrez : E, Related Sequences : R, SRS : S, Prosite : P)
  • + BEAUTY : BCM Search Launcher Proteins, Nucleic acids [D, E, R, S]
  • Cambridge (UK)
  • EBI (UK) [D] (WU and Blast2)
  • EMBL (Germany) [D] (WU)
  • EMBNet [D]
  • Submission form to the BLAST2 server at Lausanne at Expasy (Switzerland) [D], another link
  • EMBNet (Switzerland) [D]
  • GenomeNet (Japan) [D]
  • Manchester (UK)
  • Moscou (Russia)
  • Pasteur, advanced form [D]
  • Sanger (Blast and Ssaha : search on a set of protein or nucleotide databases available at the Sanger Centre)
  • Wash-U. multi-processors Pasteur [D]
  • Orthologue Blast2 (Finding orthologues & Distinguishing them from paralogues) Heidelberg (Germany)
  • Search of Arabidopsis TAIR [D, E]
  • Search of Arabidopsis (WU-Blast) TAIR (USA) [D, E]
  • Search of ASD (Alternative Splicing Database) EBI (UK)
  • Search of Bordetella Sanger (UK)
  • Search of C. elegans DatabaseSanger (UK)
  • Search of C. albicans DatabaseSanger (UK)
  • Search of DOTS (Human and Mouse Transcribed Sequences) Allgenes (USA)
  • Search of EST (EuroGeneIndexes) RBI (UK)
  • Search of Drosophila (cosmids) Sanger (UK)
  • Search of Dictyostelium Jena (Germany)
  • Search of E. Coli : Pasteur (French)
  • Search of EpoDB CBIL (USA) [D]
  • Search of Ensembl CMBI (The Netherlands)
  • Search of Fugu Ensembl
  • Search of Haemophilus influenzae LANL (USA)
  • Search of Human (selection of chromosomes) CMBI (The Netherlands)
  • Search of Human Ensembl
  • Search of Leishmania major Database Sanger (UK)
  • Search of M. leprae Sanger (UK)
  • Search of M. tuberculosis Sanger (UK)
  • Search of Merops(protease database) Sanger (UK)
  • Search of Mouse Jackson (USA)
  • Search of Mouse Ensembl
  • Search of Parasites EBI (UK)
  • Search of P. falciparum Sanger (UK), see also NCBI (USA)
  • Search of S. cerevisiae MIPS (Germany)
  • Search of S. cerevisiae Stanford (USA) [D, E]
  • Search of S. pombe Sanger (UK)
  • Search of Salmonella typhi Sanger (UK)
  • Search of Y. pestis Sanger (UK)
  • Search of Zebrafish Ensembl
  • Search of microbial genomes Sanger (follow the organism link) (UK)
  • Search of TIGR Unique Gene Indices TIGR (USA)
  • Search of UniProt EBI UK, see also PIR
  • BLITZ
  • see MPsrch EBI (UK)
  • Form at IGHM to EMBL (results by mail)
  • FASTA
  • Fasta3 CMBI (Netherlands)
  • Fasta33 EBI (UK)
  • Fasta33 Genomes EBI (UK)
  • Fasta3 (TFASTX/TFASTY, FASTF/TFASTF, FASTS/TFASTS) Virginia (USA)
  • GenomeNet (Japan)
  • IGHM (French)
  • DDBJ NIG (Japan)
  • Fasta 3 Pasteur (French), advanced
  • TBI (Germany)
  • Search of PIR PIR (USA)
  • Search of Arabidopsis TAIR (fasta 3)
  • Search of Dictyostelium Tsukuba (Japan)
  • Search of HGBASE (European SNP database : fasta3) EBI (UK)
  • Search of E. Coli Pasteur (French)
  • Search of LGIC (Ligand Gated Ion Channel Database) EBI (UK)
  • Search of PLACE (Plant Cis-acting Regulatory DNA Elements) DISC (Japan)
  • Search of S. cerevisiae Stanford (USA)
  • Species-Specific Protein Sequence Searches BCM (USA)
  • Search of NRL_3D or SwissProt PBIL (French)
  • Indiana (selection of nucleic genomic subset or selection of nucleic or proteic subset by keyword (SRS system) available)
  • Needleman and Wunsch
  • AbCheck UCL (London) test an antibody sequence against the Kabat sequence database
  • ParAlign
  • Search DNA and Protein Databases for Sequence Similarities (a.a. query sequence) Oslo (Norway)
  • ProClust : Protein Clustering - Searching for Homologue Proteins by using transitivity
  • RedHom (CPH models : finds a subset with low sequence similarity)
  • CBS (Denmark)
  • Smith et Waterman
  • Affine Smith-Waterman Algorithm Stanford (USA)
  • FDF-SW Server (Fast Data Finder) EMBNet, see also GeneMatcher EMBNet
  • MPsrch EBI (UK)
  • Search DNA and Protein Databases for Sequence Similarities (a.a. query sequence) Oslo (Norway)
  • SAMBA (Systolic Accelerator for Molecular Biological Applications) IRISA (French)
  • SCANPS (Protein Databases) EBI
  • PepPepSearch (Search of SWISS-PROT) ETH Zurich
  • SSEARCH IGHM, see also PBIL
  • SWsrch Search Service NIAS (Japan)
  • SSAHA (Sequence Search and Alignment by Hashing Algorithm)
  • Wise
  • Protein/genomic or Protein/cDNA Pasteur (French)
  • Protein vs genomic Sanger (UK)
  • From a given aminoacids composition
  • AAC
  • Entered composition and search SWISS-PROT Expasy (results by e-mail)
  • From a sequence of SWISS-PROT and search SWISS-PROT Expasy (results by e-mail)
  • MultiIdent (aa, pI, MW, sequence tag and peptide mass fingerprinting data) Expasy
  • PROPSEARCH
  • From peptides obtained by enzymatic cleavage
  • Aldente (tool to identify proteins from peptide mass fingerprinting data) Expasy
  • Mapper Manchester (UK)
  • MassDynSearch (searching SwissProt by protein mass after C or N-terminal digestion) ETHZ (Switzerland)
  • MassSearch (searching SwissProt or EMBL by protein mass after digestion) ETHZ (Switzerland)
  • MS-Fit, Tag, Edman (search GenPept, SwissProt, Owl) UCSF, see also UCSF-MSF
  • MultiIdent (aa, pI, MW, sequence tag and peptide mass fingerprinting data) Expasy
  • PeptideSearch EMBL
  • PepSeeker (a database of proteome peptide identifications for investigating fragmentation patterns) Manchester (UK)
  • Popitam (protein identification and characterization using tandem mass spectrometry data) Expasy (Switzerland)
  • Protein identification (ProFound : OWL and PepFrag : GenPept, NRL-2D, PIR, Swiss-Prot) Rockfeller (USA)
  • From pI and molecular mass
  • MultiIdent (aa, pI, MW, sequence tag and peptide mass fingerprinting data) Expasy
  • PeptIdent (pI, Mw and peptide mass fingerprinting data) Expasy
  • TagIdent (and matching a short sequence tag of up to 6 amino acids) Expasy (formely Guess-Prot)
  • From a nucleic acids sequence
  • NuclPepSearch ETHZ (search SWISS-PROT)
  • From a 3D structure
  • 3D-PSSM (Protein Fold Recognition (former Foldfit)) BMM (UK)
  • The DALI server EBI : search PDB (directly or by e-mail)
  • Finding 3-D Similarities in Protein Structures SDSC (USA)
  • SAWTED (Structure Assignment With Text Description) BMM (UK)
  • VAST (Vector Alignment Search Tool) NCBI (USA)
  • WWW server (SPASM, DEJAVU, MOLEMAN2) Uppsala (Sweden)
  • Search Databases for a pattern
  • Search protein databases
  • Arabidopsis pattern matching TAIR
  • (See BCM Launcher) BLASTPAT et FASTPAT serach a pattern database derived from “Entrez” an alignment program (PIMA) : documentation
  • Cognitor (Compare your sequence to COG database) NCBI (USA)
  • Domain Fishing (a first step in protein comparative modelling) BML (UK)
  • Halfwise (compare your DNA sequence against the whole of Pfam) Sanger (UK)
  • HMMSearch (SwissProt, NPS) PBIL (French)
  • HMM search in Pfam-A (Search the Pfam database by Hidden Markov models) Sanger, see also Washington
  • HMM Query (Search PDB or/and SCOP) UCSC (USA)
  • HMMER Pasteur (French)
  • HMMER2 Pasteur (French)
  • InterProScan (protein domains identifier) EBI (UK)
  • Kangaroo (pattern search with regular expression) BluePrint
  • Metamotif Search ISREC (Switzerland), see also Motif relation
  • MOTIF Kyoto (Japan)
  • NAIL (Network Analysis Interface for Linking HMMER results) EMBL (Germany)
  • PATOSEQ (motif search and alignment program) Expasy
  • Pattern Search : SwissProt - GenPept (ISREC) Pattern will be written with the Prosite syntax
  • Pattern Match (PIR, NRL_3D, ProClass, PATCHX, FAMBASE) PIR (USA)
  • PattinProt (Swissprot, NRL_3D, SP-TREMBL) PBIL (French)
  • ScanProsite tool (Expasy) : SwissProt Pattern will be written according the syntax of Prosite
  • Screening pattern or alignment Moscow (Russia)
  • SledgeHMMER (searching the Pfam database) Albany (USA)
  • Kangaroo (pattern search with regular expression) BluePrint
  • MAST (Motif Alignment and Search Tool) San Diego (see next MEME), see also Pasteur
  • PatMatch (Yeast Genome Pattern Matching) Stanford (USA)
  • PatScan Argonne (Proteins or Nucleic acids, selection of genomic libraries)
  • REPATT & TRANSPO (exact consecutive repeats - transposons) Barcelona (Spain)
  • Search for Sequence Pattern (DNA) PBIL (French)
  • Sig (Multiple Prosite motifs searching) Pasteur (French)
  • Signal Scan (search TDF and Transfac for eucaryotic signal) : NIH, or search IMD NIH
  • STAn (looking for nucleotidic and peptidic patterns in chromosomes) Rennes (French)

 

Nucleic acids sequences

  • Sequence Assembly
  • CAP (Contig Assembly Program Based on Sensitive Detection of Fragment Overlaps) InfoBioGen (French), see also IFOM (Italy)
  • ESSEM (Est’s aSSEmbly using Malig) LSI (Spain)
  • Gene Recognition and Assembly (GRAIL) ORNL (USA)
  • MERGER (merge two overlapping sequences) Pasteur (French)
  • Content - Codon usage - …
  • Biopolymer calculator Yale (USA)
  • Codontree (codon usage table, distance matrix and bases composition) Pasteur (USA)
  • Codon Usage Tabulated from GenBank CUTG (Japan) compilation by organism, see also Countcodon (for a sequence)
  • Codonw (Correspondence Analysis of Codon Usage) Pasteur (French)
  • Countcodon Kazusa (Japan)
  • CpG islands bioinformatics, see also EBI (UK), see also Iowa (USA)
  • CpG rich regions Pasteur, see also plot, see also newcpgseek
  • EMBOSS at Pasteur (French), see also EMBOSS at CBRG (UK)
  • Create a codon usage table CUSP
  • Codon usage statistics CHIPS
  • Codon usage table comparison CODCMP
  • Find differences (SNPs) between nearly identical sequences DIFFSEQ
  • Displays a non-overlapping wordmatch dotplot of two sequences DOTPATH
  • Displays a wordmatch dotplot of two sequences DOTTUP
  • Draws circular maps of DNA constructs CIRDNA
  • Draws linear maps of DNA constructs LINDNA
  • Synonymous codon usage Gribskov statistic plot SYCO
  • Protein pattern search after translation FUZZTRAN
  • Calculates the fractional GC content of a nucleic acid sequence GEECEE
  • Find the linguistic complexity in nucleotide sequences COMPLEX
  • Finds MAR/SAR sites in nucleic sequences MARSCAN
  • Searches DNA sequences for matches with primer pairs PRIMERSEARCH
  • Counts words of a specified size in a DNA sequence WORDCOUNT
  • Residue/base frequency table or plot FREAK
  • Display a sequence with restriction cut sites, translation etc REMAP
  • Silent mutation restriction enzyme scan SILENT
  • Reverse and complement a sequence REVSEQ
  • Wobble base plot WOBBLE
  • GCUA (Graphical Codon Usage Analyser) Regensburg (Germany)
  • JCat (to adapt codon usage of a target gene to its potential expression host) Braunschweig (Germany)
  • MSBAR (mutate sequence beyond all recognition) Pasteur (French)
  • Riche en … (graphical display of content in selected bases) ABIM (in french)
  • Verbumculus ( over- or under-represented words : suffixe tree) California (USA)
  • Map (restriction)
  • Arabidopsis Restriction Mapper TAIR (USA)
  • Find restriction sites Texas (USA)
  • NEBcutter V2.0 BioLabs
  • TACG Pasteur (French), see also California (USA)
  • Webcutter Yale, mirror at Sweden
  • Restenzyme Budapest (Hungary)
  • RESTRICT (finds restriction enzyme cleavage sites) Pasteur (French)
  • Restriction Mapper
  • Restriction Site Analysis UMMS (USA)
  • RIFLE (16S rDNA-based identification of microorganisms by comparison with RDP database restriction patterns) Bielefeld (Germany)
  • WatCut (Cleave your DNA online, and create new cleavage sites in your oligos using silent mutations) Waterloo (Canada)
  • Yeast Genome Restriction Analysis Stanford, see also Reverse Restricion Mapping (USA)
  • Microarray - Genomics
  • ACID (database for microarray clone information) Lund (Sweden)
  • Adaptive quality-based clustering of gene expression profiles Sista (Belgium)
  • Affycomp (benchmark for Affymetrix GeneChip expression measures) Johns Hopkins (USA)
  • AMPhora Expression Data Analysis MIPS (Germany)
  • Analysis tools NCGR (USA)
  • ANOVA (NIA array analysis tools) NIH (USA)
  • ArrayCyGHt (analysis and visualization of array-CGH data) Seoul (Korea)
  • ArrayPipe (a flexible processing pipeline for microarray data) Vancouver (Canada)
  • ArrayXPath (mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics) Seoul (Korea)
  • Asterias (data normalization to aCGH analysis, molecular signatures with survival data, ..) CNIO (Spain)
  • CIMMiner (generates color-coded Clustered Image Maps (CIMs) (“heat maps”) to represent “high-dimensional” data sets such as gene expression profiles) NCI (USA)
  • CONFAC (application of comparative genomic promoter analysis to DNA microarray datasets) Atlanta (USA)
  • CTWC Server (coupled two-way clustering analysis of breast cancer and colon cancer gene expression data) Weizmann (Israel)
  • eXPatGen (Gene Expression Pattern Generator) Newark (USA)
  • Express Yourself Yale (USA)
  • Expression Profiler (online platform for analysis of microarray data) EBI (UK)
  • GAP (Genome- wide Automated Primer) UCI (USA)
  • GEMS (for biclustering analysis of expression data) Boston (USA)
  • GeneCruiser (service for the annotation of microarray data) MIT (USA)
  • GenePublisher CBS (Denmark)
  • GEPAS (pipeline for microarray gene expression data) Madrid (Spain), another link
  • GOAL (automated Gene Ontology analysis of expression profiles) Ferrara (Italy)
  • INCLUSive (suite of web-based tools and is aimed at the automatic multistep analysis of microarray data) Sista (Belgium)
  • KARMA (application for comparing and annotating heterogeneous microarray platforms) Yale (USA)
  • MADTools (analysis and storage data) Nantes (French)
  • MDscan (Fast Computational Method for Finding Protein-DNA Interaction) Stanford (USA)
  • Microarray data analysis Toulouse (French)
  • Microarray gene expression data analysis tools EBI (UK)
  • Microarray Elements Search and Download TAIR (USA)
  • MIDAW (statistical analysis of microarray data) Padua (Italy)
  • Oligodb (interactive design of oligo DNA for transcription profiling of human genes) Berlin (Germany)
  • OligoWiz 2.0 (integrating sequence feature annotation into the design of microarray probes) Lyngby (Denmark)
  • Pathway Miner (extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data) Arizona (USA)
  • Prism (tool for exploring sets of genome-wide data such as the data produced by expression microarrays) Washington (USA)
  • ProbeLynx (tool for updating the association of microarray probes to genes) Vancouver (Canada)
  • ProbeWiz Server CBS (Denmark)
  • RACE (analysis computation for gene expression data) Lausanne (Switzerland)
  • ROSO (optimizing oligonucleotide probes for microarrays) PBIL (French)
  • SNOMAD (Standardization and NOrmalization of MicroArray Data) John Hopkins (USA)
  • SOTA (DNA-array data analysis) Madrid (Spain)
  • SVM (supervised cluster analysis for microarray data based on multivariate Gaussian mixture) California (USA)
  • VAMPIRE microarray suite (platform for the interpretation of gene expression data) California (USA)
  • VARAN (tool for analyzing variability amongst DNA microarrays experiments) ESPCI (French)
  • Motifs
  • CENSOR (query sequences aligned against a reference collection of human or rodent repeats) GIRI (USA)
  • Consensus (identification of consensus patterns in unaligned DNA and protein sequences) Pasteur (French)
  • CREDO (tool for computational detection of conserved sequence motifs in noncoding sequences) MIPS (Germany)
  • Emotif (find motifs in aligned sequences) Stanford (USA), see also 3motif
  • FUZZNUC (nucleic acid pattern search) Pasteur (French)
  • IWoCS (analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships) Alicante (Spain)
  • MEME (tool for discovering motifs in groups of sequences) San Diego, see also Pasteur
  • Pattern Scanning with Profiles Max-Planck (Germany)
  • Pattern_Search (searching potential composite elements similar to the COMPEL collection) GBF (Russia)
  • Probe, sequence match RDP Michigan (USA)
  • Scan_for_matches Pasteur (French)
  • SeSiMCMC (a Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length) Moscow (Russia)
  • SMILE (tool that infers motifs in a set of sequences) à Pasteur : simple motif, with 2 boxes
  • TRANSPO (Searching for Transposons with known TIR) LSI (Spain)
  • UTRScan Bari (Italy)
  • WORDMATCH (finds all exact matches of a given size between 2 DNA sequences) Pasteur (French)
  • PCR primer selection
  • Tools at Weizmann (Israel)
  • Aide PCR (in french) U-Descartes (French)
  • AcePrimer (automation of PCR primer design based on gene structure) Vancouver (Canada)
  • AMOD (a morpholino oligonucleotide selection tool) Minnesota (USA)
  • AOPredict (Antisense Oligonucleotide Prediction Program) Karolinska (Sweden)
  • ASePCR (alternative splicing electronic RT-PCR in multiple tissues and organs) Seoul (Korea)
  • Assembly PCR oligo maker (a tool for designing oligodeoxynucleotides for constructing long DNA molecules for RNA production) Toronto (Canada)
  • BiSearch (primer-design and search tool for PCR on bisulfite-treated genomes) Budapest (Hungary)
  • Cascade (16S rDNA prokaryotic multiple sequence alignment (prokMSA) for browsing, blasting, probing) LLNL (USA)
  • CloneIt (finding cloning strategies, in-frame deletions and frameshifts) INRA (French)
  • CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primers) Blocks (USA)
  • DAN (calculates DNA RNA/DNA melting temperature) Pasteur (French)
  • DEQOR (tool for the design and quality control of siRNAs) Max Planck (Germany)
  • DoPrimer (Germany)
  • Electronic PCR (PCR-based sequence tagged sites (STSs)) NCBI (USA)
  • E-RNAi (to design optimized RNAi constructs) Heidelberg (Germany)
  • ExPrimer (to design primers from exon-exon junctions) Bangalore (India)
  • FractTM (a fractional programming approach to efficient DNA melting temperature calculation) Koln (Germany)
  • Gene2Oligo (oligonucleotide design for in vitro gene synthesis) Michigan (USA)
  • GeneFisher Bielefeld (Germany)
  • G-PRIMER (greedy algorithm for selecting minimal primer set) Singapore
  • Hyther WSU (USA)
  • ISOCHORE (plots isochores in large DNA sequences) Pasteur (French)
  • MEDUSA Karolinska (Sweden)
  • MELTING (enthalpie, entropy and melting temperature) Pasteur (French)
  • MethPrimer (Design Primers for Methylation PCRs) UCSF (USA)
  • MuPlex (multi-objective multiplex PCR assay design) Boston (USA)
  • Oligo Calculator (Java script) Pittsburg (USA)
  • Oligo Calculator BioInf (USA)
  • Oligodb (interactive design of oligo DNA for transcription profiling of human genes) Berlin (Germany)
  • OligoFAktory (a visual tool for interactive oligonucleotide design) Brussells (Belgium)
  • PCR designer for restriction analysis of various types of sequence mutation Oxford (UK)
  • PCR Suite (Overlapping_Primers, Genomic_Primers, SNP_Primers, cDNA_Primers) Rotterdam (The Netherlands)
  • PIRA (PCR designer for restriction analysis of single nucleotide polymorphisms) Southampton (UK)
  • PRIDE (PRImer DEsign for large scale sequencing) TBI (Germany)
  • PriFi (using a multiple alignment of related sequences to find primers for amplification of homologs) Aarhus (Denmark)
  • PRIMA (selects primers for PCR and DNA amplification) Pasteur (French)
  • Primaclade (a flexible tool to find conserved PCR primers across multiple species) Saint Louis (USA)
  • Primegens (PRIMEr Design Using GEN Specific Fragments) ORNL (USA)
  • Primer 3 MIT (USA), see also UMMS (USA)
  • The Primer Generator Johns Hopkins (USA)
  • Primo (Prediction of forward and reverse oligonucleotide Primers) Pasteur (French), see also Texas
  • Primo MSP (methylation specific PCR Primer design) Chang Bioscience
  • Radiation Hybrid Mapping MIT (USA)
  • SIDE (siRNA design, highly specific and accurate selection of siRNAs for high-throughput functional assays) Madrid (Spain)
  • siDirect (target-specific siRNA design software for mammalian RNA interference) Tokyo (Japan)
  • siRNA selector Philadelphia (USA)
  • siRNA Design Tool (filtering, …) Hong Kong (UK)
  • SNPbox (primer design from gene to genome) Antwerp (Belgium)
  • SNP Cutter (a comprehensive tool for SNP PCR-RFLP assay design) Chicago (USA)
  • SOP3v2 (selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms) Pittsburgh (USA)
  • SSR primer (simple sequence repeat marker loci discovery) Victoria (Australia)
  • STSSEARCH (searches a DNA database for matches with a set of STS primers) Pasteur (French)
  • TROD (short interfering RNAs (siRNAs) with T7 RNA polymerase) Genève (Switzerland)
  • VecScreen (tool for screening a nucleotide sequence for vector) NCBI (USA)
  • Virtual PCR Brno (Czech Republic)
  • vPCR Padua (Italy)
  • WatCut (Cleave your DNA online, and create new cleavage sites in your oligos using silent mutations) Waterloo (Canada)
  • Web Primer (Saccharomyces) Stanford
  • Bellerophon (detects chimeric sequences in multiple sequence alignments 16S rDNA) Brisbane (Australia)
  • Chimera detection (Detection of chimeric 16S rRNA artifacts generated by PCR amplification) USC (USA)
  • Prediction of gene structure (exons, splicing sites, promotors)
  • AAT (Analysis and Annotation Tool for Finding Genes in Genomic Sequences) Michigan (USA)
  • AGenDA (gene-prediction tool that is based on cross-species sequence comparison) Bielefeld (Germany)






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