Bioinformatics Tools List
DNA Sequence Analysis Tools
| § 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) | |
| § 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) | |
| § 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 GeneMarkat 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) | § Gene feature (Exon recognition, Promoter and Transcription Factor Binding Site Prediction, Open Reading Frame Identification.at Baylor College of Medicine (USA): |
| § Identification of Prokaryotic Promoters(Promotor prediction in <100 kb DNA at Lawrence Berkeley National Laboratory, USA) § IHF Site/Sigma 54 Promoter searches (at Pensylvania State University, USA) | § SignalScan (Identification of transcriptional elements in <100 kb DNA sequences < 100 kb at BIMAS, University of Minesota, USA) |
| § tRNAscan-SE (Search for tRNA genes in genomic sequence at Washington University, St Louis, US) | |
| § 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 | § 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) |
Protein Function Assignment
| § 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 CDDdomain 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) § 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) | § 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) § InterProScan or InterPro Search (Search a protein against the integrated protein domains and functional sites database InterPro at EBI, UK) § iProCass Search (Search a protein against PIR's integrated protein class database at Georgetown University, USA) § MEME (Multiple EM for Motive Elicitation: Motive discovery at San Diego Supercomputer Centre, SDSC, Ca, USA) § 3Motif (Find protein (domain)s with defined 3D motifs at Stanford University, USA (runs only with Netscape and Chime plugin)) |
| § KEGG (Search and computation tools at KEGG pathway database, Kyoto, Jp) | |
| § DIP (Search Database of Interacting Proteins at UCLA, USA) § PreBIND (Locate biomolecular interaction information in the scientific literature at theSamuel Lunenfeld Research Institute, Toronto, Canada ) § BINDBLAST (Search BIND database with BLAST) | § BIND (Biomolecular Interaction Network Database at the Samuel Lunenfeld Research Institute, Toronto, Canada ) |
| § PAA (Protein Annotator's Assistant at EBI, UK) § Artemis (Free (large-) DNA sequence viewer and annotation tool at the Sanger Center, UK) | |
| § 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) | § 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) |
| § RNA Fold (Fold your own RNA sequences) | |
Protein sequence & Structure
| § ProtParam (Calculate aa comp, MW, pI, extinction coefficient at ExPASy, CH) | |
| § 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) | § 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) |
| § 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) | § Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA) |
| § 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) | § HMMTOP (Prediction of transmembrane helices and topology of proteins at Hungarian Academy of Sciences) |
Posts
