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AnalysisMicroarray
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NCBI - National Center for Biotechnology Information (GenBank) |
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EBI - European Bioinformatics Institute (EMBL) |
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EMNEW - Index of New EMBL Sequences ( EBI) |
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DDBJ - DNA Data Bank of Japan |
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SWISS-PROT- Protein sequence database |
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SWISSNEW - New SwissProt Sequence Entries @ EBI |
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PIR - Protein Information Resource |
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MIPS - Munich Information centre for Protein Sequences |
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BLAST -Basic local alignment search tool @ NCBI |
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Blast Search @EBI |
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Blast Search @Expasy |
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Blast Search @ISREC |
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Blast Search @Pasteur Institute , France |
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PSI BLAST -Position Specific Iterated Blast search @ NCBI |
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C. elegans Blast Server @ Sanger Centre: Sear |
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FASTA Fasta or fastx search @ EBI |
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BLAST Microbial Genomes -Genomic sequences search @ NCBI |
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MPsrch -Smith-Waterman algorithm-based search |
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BLASTPAT - BLAST-based Pattern Database Search |
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FASTPAT - FASTA-based Pattern Database Search |
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SectionSearch -FastA or TFastA search against predefined Sequence database |
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WU-BLAST Archives - Washington University School of Medicine, St. Louis |
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UNIBLAST - BLAST Against Organism specific Sequences |
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THC-Blast - Tentative Human Consensus Sequences BLAST |
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ClustalW- Multiple Sequence alignment @ EBI, UK |
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ClustalW - Multiple Sequence alignment @ Baylor College of Medicine, USA |
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ClustalW -Multiple sequence alignment @ WUSTL, USA |
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Match-Box Multiple sequence alignment Tool @ Belgium |
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Align -Pairwise sequence alignment |
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MAP -Multiple alignment of (long) sequences without penalizing large gaps |
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CINEMA- Color INteractive Editor for Multiple Alignments at BCM group, UK |
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AMAS -Analyze multiple aligned sequences at Oxford University, UK |
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BEAUTY - BLAST Enhanced Alignment Utility |
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BOXSHADE - Printing and shading of multiple alignments |
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Alignment Utilities Alignment and create the consensus alignment |
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MSA 2.1 -Optimal multiple alignment using the Carrillo-Lipman method |
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SIM4 - Align cDNA and Genomic DNA |
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Wise2 -Align protein genomic sequence to predict a gene structure |
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PipMaker - Alignments of similar regions in two long DNA sequences |
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T-COFFEE - Multiple sequence alignment tool, CNRS France |
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VISTA - Align and find conserved regions in Genomic sequences |
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SAM - Sequence Alignment and Modeling System @ UCSC |
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3DB Browser -Structure database browser @ Weizmann Institute of Science, Israel |
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3DCrunch -Database Browser of modeled Swiss-Prot proteins at ExPASy, Switzerland |
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3D-Jigsaw -Comparative modeling server |
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AAT- Analysis and Annotation Tool for finding genes in genomic sequences |
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ASC -Analytic Surface Calculation of PDB molecules @t EMBL, Heidelberg) |
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BIND -Biomolecular Interaction Network Database |
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BLOCKS Search -Search a protein against BLOCKS database |
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BTPRED -Prediction of beta-turns |
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CD-Search-Search a protein against CDD domain database |
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Chime - Plugin for structure view |
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Cn3D-Plugin for structure view for structure @ NCBI |
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COGnitor - Search a protein against the COG database |
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eMOTIF Search -Assign putative function to new proteins by sequence comparison with IDENTIFY motif database. |
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Coils -Prediction of coiled Coil regions by Lupas' method |
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CPHmodels-Structure prediction by comparative homology modeling |
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DAS -Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method @ Stockholm University |
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DGPI - Prediction of GPI-anchor and cleavage sites |
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DIP -Search Database of Interacting Proteins |
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DOMO - Homologous protein domain families database |
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DOMPLOT -Structural domain organization annotated by ligand contacts. |
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eMATRIX Search - Predict function by sequence analysis using minimal-risk scoring matrices. |
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eMOTIF Maker - Generate motifs describing protein families or superfamilies |
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FAMS -Fully Automated Modeling Service |
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FingerPRINTScan -Search a protein sequence against protein motif fingerprints database |
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Helical Wheel - Represents alpha-helical peptides |
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HMMTOP - Prediction of transmembrane helices and topology of proteins |
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HNN - Hierarchical Neural Network secondary structure prediction |
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Hydropathy plots - Plot Hydropathy |
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InterPro Search -Search a protein against the integrated protein domains and functional sites |
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JPred - Protein secondary structure prediction |
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LIBRA - LIght Balance for Remote Analogous proteins: search compatible structure of a target sequence by threading |
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List of comparative modeling tools |
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LOCK Compare 3D structures of query and target proteins and their visualization of superposed |
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Modules -Mobile protein domains database |
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MolSurfer -Calculate and navigate protein-protein interfaces |
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MultiCoil -Prediction of coiled coil regions as dimeric or trimeric assemblies |
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NetOGlyc - Prediction of O-glycosylation sites in mammalian proteins |
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NetPhos -Prediction of phosphorylation sites in eukaryotic proteins |
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nnPredict -Protein secondary structure prediction. |
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PAA - Protein Annotator's Assistant |
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PairCoil -Prediction of coiled Coil regions. |
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PFSCAN -Protein search against different profile databases |
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PPSearch -Search a protein sequence against prosite pattern database |
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Predator -Secondary structure prediction from single or multiple sequences at EMBL, Heidelberg |
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Predicting Protein 3D structure based on homologous sequence search |
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PredictProtein -Protein secondary structure prediction at EMBL |
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PROCAT - Search a protein structure agains the procat database of 3D enzyme active site templates |
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ProDom - Protein domain database |
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ProNet Online -Database of interacting proteins |
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PROSCAN -Search a protein sequence against prosite pattern database |
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ProtColourer - Draw colour-coded representation of an amino acid sequence |
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ProTherm -Thermodynamic Database for Proteins and Mutants |
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ProtParam -Calculate aa comp, MW, pI, extinction coefficient |
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ProtScale -Hydrophobicity and other conformational parameters. |
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PSIpred -Protein secondary structure prediction |
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PSort -Prediction of signal sequence, transmembrane regions and protein localization |
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PSort -Prediction of signal sequence, transmembrane regions and protein localization. |
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RasMol 3D viewer |
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SAPS -Statistical Analysis for charged clusters, repeats, hydrophobic regions, compositional domains |
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SBASE - Protein domain library |
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ScanProsite - Search a protein sequence against prosite pattern database |
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Scansite - Prediction of protein signaling sequence motifs |
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SDSC1 - Protein structure homology modeling server |
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SignalP - Prediction of peptide signal sequence |
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SOSUI -Prediction of Transmembrane Regions |
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STRUCTURE -Molecular Modeling Database MMDB |
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Swiss-Model -Automated protein modeling server |
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Swiss-Pdb Viewer - 3D viewer |
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TargetP -Prediction of subcellular localization |
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TMHMM -Prediction of transmembrane helices in proteins |
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TMpred - Prediction of membrane-spanning regions and their orientation |
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TOPS -Protein topology cartoon generation |
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VAST - Structure-structure similarity search |
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WebMol - 3D viewer |
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CENSOR-Query Sequence Comparison against Human/Rodent Repeats Database |
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Gene Finder -Exon and Splice Site Prediction |
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GENEID -Prediction of Exons and Gene Structure |
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GenHunt -Exon Search |
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GENIE - Gene Finder |
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GenLang -Gene Structure & Transcriptional Element Features Prediction |
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GRAIL - Exon Prediction |
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HCpolyA - Poly-A Site Prediction |
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HCtata -TATA Signaling Prediction |
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HEXON - Prediction of Internal Exons in Human DNA |
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MatInspector - Transcription Factor Binding Sites prediction |
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McPromoter-Prediction of Transcription Start Sites in Eukaryotic DNA |
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NNPP- Promoter Prediction |
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NNSSP -Splice Site Prediction by Neural Network |
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ORD ID - Open Reading Frame search |
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ORF Finder - Open Reading Frame Finder |
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ORFGene -Gene Structure Prediction |
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PatScan - DNA Sequence Motif search |
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Pol3Scan -tRNA Genes Search |
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POLYA-Search for of 3'-end Cleavage & Poly-A Signals |
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PROCRUSTES - Gene Recognition |
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PYTHIA - Human Repetitive DNA Analysis |
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RepEater - Search for Repeats |
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RepeatMasker2 - Search for Repetitive Elements in DNA Sequences |
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Signal Scan - Search for Eukaryotic Transcriptional Elements |
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Splice Site -Splice Site Prediction |
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SpliceView - Splice Signals Prediction |
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Target Finder - Identification of target genes of DNA-binding proteins |
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TESS - Transcription Factor Binding Site Sequence Search |
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Tfsitescan - Promoter Analysis |
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tRNAscan - tRNA Gene Search |
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YSPL (BCM Gene Finder) - Exon-Exon Junction Positions Search in cDNA |
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Translation Tool - Protein Translation |
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The Protein Machine - Protein Translation |
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6 Frame Translation Tool - Translate DNA Sequence in all 6 Frames |
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Reverse Translation Tools - Reverse Complement |
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Primer - Design Primers in Query Sequence |
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Primer3- |
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NetPrimer - Online / Offline Primer designing |
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Primerfinder - Primer Designing Tool |
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WEB Cutter -Restriction Analysis of Query Sequence |
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ENZFINDER- Restriction analysis Tool at Molecular Biology Shortcuts |
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Silent Restriction Sites Identification - Create a New Restriction Site Without changing the amino acid |
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TACG- Restriction Analysis Tool |
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Expression Profiler- Analysis of microarray data |
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ClustArray-DNA microarray data analysis |
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TBI Expression Analysis -Search for differential genes |