生物信息在线分析工具汇总
转载请注明来自丁香园
生物信息学所涉及软件之多，现将常用软件罗列如下（均为在线工具），很是方便。
- Search a sequence database
- Nucleic acids sequences
- Patterns (proteins)
- Prediction on protein sequences
- Alignments - Phylogeny
- Analysis tools package
Search a sequence database - menu
- 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)
- NCBI [E]
- Gapped BLAST (résultats avec liens Banques : D, Entrez : E, Related Sequences : R, SRS : S, Prosite : P)
- Advanced Form EMBNet [D]
- Basic Form EMBNet, see also Expasy [D]
- Pasteur, advanced form [D]
- Search of microorganisms U-ParisSud (French)
- Search of PIR PIR [D]
- 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
- 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
- Koln (Germany)
- 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)
- Trace server Ensembl
- Wise
- BLAST (results with links Databases : D, Entrez : E, Related Sequences : R, SRS : S, Prosite : P)
- 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
- CBS (French)
- AAC
- 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)
- Search protein databases
Nucleic acids sequences - menu
- 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)
作者: alexru
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