Analysis Tools and Web Servers
Categories
Bioinformatics Links
DNA Sequence Analysis Tools
Restriction, Detect repeats & unsual Patterns |
- Webcutter (Restriction analysis)
- RepeatMasker (Search interspersed repeats and low complexity sequences)
- dnadot (Find regions of similarity in two sequences and repeats within a single sequence at Colorado State University, USA)
- LALIGN (Finds multiple matching subsegments in two sequences at EMBnet, Swiss node)
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- Tandem Repeats Finder (at Mount Sinai School of Medecine, NY, USA)
- Dot Plot (Compare a large sequence with itself at Virtual Genome Center)
- Blast 2 Sequences (Compare two sequences <150 kb to trace repeat sequences)
- Zinfo (Detection of unusual sequences in large DNAs at Virtual Genome Center), USA)
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- Align (Pairwise sequence alignment with GAP, SIM (DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)
- ClustalW (at EBI, UK)
- Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)
- CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)
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- MAP (Multiple alignment of (long) sequences without penalizing large gaps)
- ClustalW (Multiple sequence alignment at WUSTL, USA)
- ClustalW (at the Baylor College of Medicine, USA)
- AMAS (Analyze multiple aligned sequences at Oxford University, UK)
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- Webtrans (Translation and codon usage of very large sequences at Virtual Genome Center)
- GeneMark (Species-specific search for genes with WebGeneMark , WebGeneMark.hmm and Heuristic GeneMark at Georgia Institute of Technology , USA)
- GenLang (Exon recognition at University of Pennsylvania, USA)
- GeneMachine (Integrated comparative and predictive gene identification at NHGRI, USA)
- AAT (Analysis and Annotation Tool for finding genes in genomic sequences at Michigan Tech, USA)
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- Sixframe (Translate DNA sequence in all 6 possible frames)
- ORF Finder (at NCBI)
- GeneMark (Species-specific search for genes cfr. WebGeneMark at EBI, UK)
- GRAIL (Exon recognition USA).
- Gene feature (Exon recognition, Promoter and Transcription Factor Binding Site Prediction, Open Reading Frame Identification.at Baylor College of Medicine (USA):
- NetPlantGene (Prediction of splice sites in Arabidopsis at CBS, Denmark)
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Find Transcriptional elements |
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- SignalScan (Identification of transcriptional elements in <100 kb DNA sequences < 100 kb at BIMAS, University of Minesota, USA)
- FirstEF (first-exon and promoter prediction program for human DNA at CSHL, USA)
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- tRNAscan-SE (Search for tRNA genes in genomic sequence at Washington University, St Louis, US)
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- FAStRNA (Predict potential tRNA genes in genomic sequences at Institut Pasteur, Paris, France)
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- CountCodon (Analyse codon usage in protein coding sequence at Kazuasa DNA Research Institute, Jp)
- DNA folding server (Fold secondary structures)
- Netprimer (Free online primer analysis at Premier Biosoft Int., Ca, USA)
- IMGT/V-QUEST an interactive tool for immunoglobulin and T cell receptor sequence analysis
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- MAR-Finder (Search for matrix association regions at NCGR, Santa Fe, USA)
- Reverse Complement (Convert DNA sequence data to it's Reverse Complement.)
- PRIDE (Primer design atDFKZ, Heidelberg, Germany)
- PCR primer selection
Primer3 (PCR primer selection tool at Whitehead Institute for Biomedical Research, US)
GeneFisher (Interactive PCR primer design tool at the University of Bielefeld, Germany)
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Protein Function Assignment
Search Pattern, motif, Profiles domains, families |
- ScanProsite (Search a protein sequence against PROSITE pattern database at ExPASy, CH)
- PPSearch (Search a protein sequence against PROSITE pattern database with graphical output at EBI, UK)
- FingerPRINTScan (Search a protein sequence against protein motif fingerprints database PRINTS )
- Scansite (Prediction of protein signaling sequence motifs at HIM, Boston, USA)
- SearchPfam at Wustl or EBI (Search a protein against Pfam domain/family database)
- CD-Search (Search a protein against CDD domain database, including Pfam and SMART, with RPS-BLAST at NCBI, USA)
- eMOTIF Search (Assign putative function to new proteins by sequence comparison with IDENTIFY motif database at Stanford University, USA)
- PROCAT (Search a protein structure agains the PROCAT database of 3D enzyme active site templates)
- Meta-MEME (motive buiding at San Diego Supercomputer Centre, SDSC, Ca, USA)
- eMOTIF Maker (Generate motifs that describe protein families or superfamilies ats Stanford University, USA)
- Modules (mobile protein domains database)
- HSSP (Database of homology-derived structures and sequences of proteins at EBI)
- eMATRIX Search (Function prediction by sequence analysis using minimal-risk scoring matrices at Stanford University, USA)
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- PROSCAN (Search a protein sequence against PROSITE pattern database allowing mismatches at PBIL, Lyon, Fr)
- PFSCAN (Search protein against different profile databases at ISREC; also searches PROSITE and Pfam patterns)
- BLOCKS Search (Search a protein against BLOCKS database; also searches PRINTS)
- DART (Domain Architecture Retrieval Tool at NCBI, USA)
- InterProScan or InterPro Search (Search a protein against the integrated protein domains and functional sites database InterPro at EBI, UK)
- COGnitor (Search a protein agains the COG database at NCBI)
- iProCass Search (Search a protein against PIR's integrated protein class database at Georgetown University, USA)
- SMART (Simple Modular Architecture Research Tool at EMBL; also searches Pfam)
- MEME (Multiple EM for Motive Elicitation: Motive discovery at San Diego Supercomputer Centre, SDSC, Ca, USA)
- ProDom (Protein domain database at Toulouse, Fr)
- DOMO (homologous protein domain families database)
- SBASE (Protein domain library at ICGEB, It)
- 3Motif (Find protein (domain)s with defined 3D motifs at Stanford University, USA (runs only with Netscape and Chime plugin))
- GeneQuiz (Automated analysis of protein sequences at EMBL)
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Search, computation & analysis of pathways |
- KEGG (Search and computation tools at KEGG pathway database, Kyoto, Jp)
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- aMAZE (Query tools for pathway analysis at EBI, UK)
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Protein-Protein interactions |
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- PAA (Protein Annotator's Assistant at EBI, UK)
- Artemis (Free (large-) DNA sequence viewer and annotation tool at the Sanger Center, UK)
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Automatic alert for related new sequence |
- Sequence Alerting System (E-mail alert for daily searched new homologues of query sequence at EMBL, Heidelberg)
- Swiss-Shop (Automatically receive alerts upon new submissions of related protein sequences)
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- PubCrawler (Automated alerting service that scans daily updates to PubMed and GenBank databases at Trinity College Dublin, Ireland)
- Microbial Genomes Notification (Receive notifications by e-mail about new complete genomes in GenBank)
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- RNA World (Links to RNA resources from IMB Jena Biocomputing Group, Jena, Germ.)
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Protein sequence & Structure
Physiochemcial Properties |
- ProtParam (Calculate aa comp, MW, pI, extinction coefficient at ExPASy, CH)
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- ProTherm (Thermodynamic Database for Proteins and Mutants, Jp)
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- ProtColourer (Make colour-coded representation of an amino acid sequence at EBI)
- ProtScale (Hydrophobicity, other conformational parameters, etc. at ExPASy)
- SignalP (Prediction of peptide signal sequence at CBS, Denmark)
- TargetP (Prediction of subcellular localization at CBS, Denmark)
- NetOGlyc (Prediction of O-glycosylation sites in mammalian proteins at CBS, Denmark)
- NetPhos (Prediction of phosphorylation sites in eukaryotic proteins)
- Helical Wheel (Representation of alpha-helical peptides)
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- Hydropathy plots (At Pensylvania State University, Department of Biochemistry and Molecular Biology)
- SAPS (Statistical Analysis for charge clusters, repeats, hydrophobic regions, compositional domains etc. at ISREC, CH)
- PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
- DGPI (Prediction of GPI-anchor and cleavage sites, University of Geneva, CH)
- Scansite (Prediction of protein signaling sequence motifs at HIM, Boston, USA)
- Other primary sequence analysis tools at ExPaSy
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- Blast 2 Sequences (Alignment of two protein sequences using BLAST at NCBI, USA)
- ClustalW (Multiple sequence alignement at WUSTL, USA)
- Align (Pairwise sequence alignment with GAP, SIM (DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)
- AMAS (Analyze multiple aligned sequences at Oxford University, UK)
- CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)
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- SIM (Alignment of 2 protein sequences at ExPASy, Switzerland)
- ClustalW (at EBI, UK)
- ClustalW (at the Baylor College of Medicine, USA)
- MAP (Multiple alignment of (long) sequences without penalizing large gaps
- Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)
- BOXSHADE (Software for visual information on aligned regions at ISREC, Switzerland)
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Predict Secondary Structure |
- TMpred (Prediction of membrane-spanning regions and their orientation at ISREC)
- SOSUI (Prediction of Transmembrane Regions, JP)
- DAS (Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method, Stockholm University)
- TopPred2 (Topology prediction of membrane proteins at the Institut Pasteur, Paris, France)
- JPred (Protein secondary structure prediction at EBI)
- HNN (Hierarchical Neural Network secondary structure prediction at NPS@, Lyon, France)
- nnPredict (Protein secondary structure prediction at UCSF, CA, USA)
- BTPRED (Prediction of beta-turns at UCL, UK)
- PairCoil (Prediction of coiled Coil regions, Bergers method)
- TOPS (Protein topology cartoon generation at EBI, UK)
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- TMHMM (Prediction of transmembrane helices in proteins at CBS, Denmark)
- PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
- HMMTOP (Prediction of transmembrane helices and topology of proteins at Hungarian Academy of Sciences)
- PredictProtein (Protein secondary structure prediction at EMBL)
- Predator (Secondary structure prediction from single or multiple sequences at EMBL, Heidelberg)
- PSIpred (Protein secondary structure prediction at Brunel University, UK)
- Other secondary structure prediction tools at ExPASy
- Coils (Prediction of coiled Coil regions Lupas' method at EMBnet-CH)
- MultiCoil (Prediction of coiled coil regions as dimeric or trimeric assemblies at WI , USA)
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Analyse & Model 3D Structure
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- RasMol (Free offline 3D viewer. Download )
- Chime (Browser plugin for structure view from MDL Chemscape)
- Cn3D (Browser plugin for structure view used in ENTREZ/STRUCTURE from NCBI)
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- DOMPLOT (Generate schematic diagrams of the structural domain organisation annotated by ligand contacts at University College London, UK)
- GenTHREADER (Sequence profile based fold recognition on PSIpred server at Brunel University, UK)
- 123 (Fold prediction by aligning (threading) to a (set of) structure(s)
- DALI (Automated Protein Structure Alignment at EBI,UK)
- LIBRA (LIght Balance for Remote Analogous proteins: search compatible structure of a target sequence by threading at NIG, Jp)
- MolSurfer (Calculate and navigate protein-protein interfaces at EMBL, Heidelberg)
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- CPHmodels (Structure prediction by comparative homology modeling at CBS, Denmark)
- 3DCrunch (Browse database of modeled Swiss-Prot proteins at ExPASy, Switzerland)
- SDSC1 (Protein structure homology modeling server at SDSC, USA)
- List of comparative modeling tools (at the Rockefeller University, NY, USA)
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- Swiss-Model (Automated protein modeling server at ExPASy, Switzerland)
- FAMS (Fully Automated Modeling Service at Kitasato University, JP)
- 3D-Jigsaw (Comparative modeling server at Imperial Cancer Research Fund, London, UK )
- Meta PP (Collection of structure prediction services at Columbia University, USA)
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Phylogenetic Analysis
Mutiple sequence alignment |
- ClustalW (Multiple sequence alignement at WUSTL, USA)
- Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)
- BOXSHADE (Software for visual information on aligned regions at ISREC, Switzerland)
- TaxPlot (3-way comparisons of genomes based on encoded proteins at NCBI)
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- ClustalW (at EBI, UK)
- ClustalW (at the Baylor College of Medicine, USA).
- AMAS (Analyze multiple aligned sequences at Oxford University, UK).
- Entrez-PopSet (Search set of DNA sequences from populations of related individuals/organisms at NCBI)
- Phylogeny software
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Microarray data analysis
Attribution: Content of this site were compiled through various rich resources available on internet,Few major resources are as follows:
1) Suresh Kumar (2005). Bioinformatics web. Retrieved June 11, 2008 from: http://www.geocities.com/bioinformaticsweb/
2) http://archive.gersteinlab.org/mark/cbb752-spr09/cbb752-mg-spr09-bioinfo-intro.ppt
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Creative Commons Attribution-NonCommercial-NoDerivs 2.5 License
