Tools
| Molecular Biology Tools Classified by | |||
| - Protein
identification and characterization - Transcription/Traslation Tools - Similarity searches - Pattern and profile searches - Post-translational modification prediction |
- Primary structure
analysis - Secondary structure prediction - Tertiary structure prediction - Transmembrane regions detection - Sequence Alignment |
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| Protein identification and
characterization + AACompIdent : Identify a protein by its amino acid composition + AACompSim : Compare the amino acid composition of a SWISS-PROT entry with all other entries + CombSearch An experimental unified interface to query several protein identification tools accessible on the web + FindMod Predict potential protein post-translational modifications and potential single amino acid substitutions in peptides. Experimentally measured peptidemasses are compared with the theoretical peptides calculated from a specified SWISS-PROT entry or from a user-entered sequence, and mass differences are used to better characterize the protein of interest + FindPept Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage + GlycanMass : Calculate the mass of an oligosaccharide structure + GlycoMod Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses + Mascot Peptide mass fingerprint, sequence query and MS/MS ion search from Matrix Science Ltd., London + MultiIdent Identify proteins with pI, Mw, amino acid composition, sequence tag and peptide mass fingerprinting data + PepSea Protein identification by peptide mapping or peptide sequencing from Protana, Denmark + PeptideCutter Predicts potential protease and cleavage sites and sites cleaved by chemicals in a given protein sequence + PeptideMass Calculate masses of peptides and their post-translational modifications for a SWISS-PROT or TrEMBL entry or for a user sequence + PeptIdent Identify proteins with peptide mass fingerprinting data, pI and Mw Experimentally measured, user-specified peptide masses are comparedwith the theoretical peptides calculated for all proteins in SWISS-PROT, making extensive use of database annotations + PeptideSearch : Peptide mass fingerprint tool from EMBL Heidelberg + Phenyx : Phenyx is a software platform for the identification and characterization of proteins and peptides from mass spectrometry data. Developed by GeneBio in collaboration with the Swiss Institute of Bioinformatics (SIB) and incorporating the true probabilistic and flexible scoring system OLAV developed at GeneProt Inc., Phenyx is specifically designed to meet the concurrent demands of high-throughput MS data analysis and dynamic high quality results assessment. + ProteinProspector A variety of tools from UCSF (MS-Fit, MS-Tag, MS-Digest, etc.) for mining sequence databases in conjunction with mass spectrometry experiments + PROWL Protein chemistry and mass spectrometry resource from Rockefeller and NY Universities + TagIdent Identify proteins with pI, Mw and sequence tag, or generate a list of proteins close to a given pI and Mw |
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Transcription/Traslation
Tools |
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| Similarity searches
+ Bic ultra-fastrigorous (Smith/Waterman) similarity searches using the Bioccelerator + DeCypher Smith/Waterman or FrameSearch search using the DeCypher hardware accelerator + Fasta3 : FASTA version 3 at the EBI + FDF : Smith/Waterman type searches on Paracel's Fast Data Finder (FDF) at EMBnet-CH + PropSearch; searches for structural homologs using a 'properties' + SAMBA : Systolic Accelerator for Molecular Biological Applications + SAWTED : Structure Assignment With Text Description + Scanps : Similarity searches using Barton's algorithm |
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| Pattern and profile searches + Frame-ProfileScan : Scans a short DNA sequence against protein profile databases + Hits : Relationships between protein sequences and motifs + InterPro Scan Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases + PATTINPROT Scans a protein sequence or a protein database for one or several pattern(s)BIL + Pfam HMM search scans a sequence against the Pfam protein families databases + PPSEARCH : Scans a sequence against PROSITE (allows a graphical output); at EBI + PRATT : Interactively generates conserved patterns from a series of unaligned proteins + ProfileScan : Scans a sequence against protein profile databases + PROSITE scan : Scans a sequence against PROSITE (allows mismatches); at PBIL + ScanProsite Scans a sequence against PROSITE or a pattern against SWISS-PROT and TrEMBL + SMART : Simple Modular Architecture Research Tool; at EMBL + TEIRESIAS Generate patterns from a collection of unaligned protein or DNA sequences; at IBM |
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| Post-translational modification
prediction + big-PI Predictor : GPI Modification Site Prediction + ChloroP : Prediction of chloroplast transit peptides + DGPI : Prediction of GPI-anchor and cleavage sites + DictyOGlyc : Prediction of GlcNAc O-glycosylation sites in Dictyostelium + MITOPROT: Prediction of mitochondrial targeting sequences + NetOGlyc : Prediction of type O-glycosylation sites in mammalian proteins + NetPhos : Prediction of Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins + NetPicoRNA : Prediction of protease cleavage sites in picornaviral proteins + Predotar : Prediction of mitochondrial and plastid targeting sequences + PSORT : Prediction of protein sorting signals and localization sites + SignalP : Prediction of signal peptide cleavage sites + Sulfinator : Prediction of tyrosine sulfation sites + TargetP : Prediction of subcellular location + YinOYang : O-beta-GlcNAc attachment sites in eukaryotic protein sequences |
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| Primary structure analysis
+ Coils : Prediction of coiled coil regions in proteins (Lupas's method) at EMBnet-CH + Colorseq : Tool to highlight (in red) a selected set of residues in a protein sequence + Compute pI/Mw Compute the theoretical pI and Mw from a SWISS-PROT or TrEMBL entry or for a user sequence + Drawhca : Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence + HelixWheel/ HelixDraw : Representations of a protein fragment as a helical wheel + HLA_Bind : Prediction of MHC type I (HLA) peptide binding + Multicoil : Prediction of two- and three-stranded coiled coils + MW, pI, Titration curve : Computes pI, composition and allows to see a titration curve + Paircoil: Prediction of coiled coil regions in proteins (Berger's method) + PEST : Identification of PEST regions + PESTfind : Identification of PEST regions at EMBnet Austria + Protein Colourer : Tool for coloring your amino acid sequence + ProtParam Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.) + ProtScale Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.) + RandSeq : Random protein sequence generator + REP : Searches a protein sequence for a repeats + SAPS : Statistical analysis of protein sequences at EMBnet-CH + SYFPEITHI : Prediction of MHC type I and II peptide binding |
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| Secondary structure prediction + AGADIR : An algorithm to predict the helical content of peptides + Prof : Cascaded Mutiple Classifiers for Secondary Structure Prediction + GOR I (Garnier et al, 1978) [At PBIL or at SBDS] + GOR III (Gibrat et al, 1987) + GOR IV (Garnier et al, 1996) + HNN : Hierarchical Neural Network method (Guermeur, 1997) + Jpred : A consensus method for protein secondary structure prediction at EBI + NnPredict : University of California at San Francisco (UCSF) + PredictProtein PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec from Columbia University + PSA : BioMolecular Engineering Research Center (BMERC) / Boston + PSIpred : Various protein structure prediction methods at Brunel University + SOPM (Geourjon and Del?ge, 1994) + SOPMA (Geourjon and Del?ge, 1995) |
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| Tertiary structure prediction + 3D-PSSM Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure information (Foldfit) + CPHmodels : Automated neural-network based protein modelling server + Geno3d : Automatic modelling of protein three-dimensional structure + SWEET : Constructing 3D models of saccharids from their sequences + SWISS-MODEL : An automated knowledge-based protein modelling server + Swiss-PdbViewer : A program to display, analyse and superimpose protein 3D structures |
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| Transmembrane regions detection + DAS Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University) + HMMTOP Prediction of transmembrane helices and topology of proteins (Hungarian Academy of Sciences) + PredictProtein : Prediction of transmembrane helix location andtopology (Columbia University) + SOSUI : Prediction of transmembrane regions (TUAT; Tokyo Univ. of Agriculture & Technology) + TMAP Transmembrane detection based on multiple sequence alignment (Karolinska Institut; Sweden) + TMHMM : Prediction of transmembrane helices in proteins (CBS; Denmark) + TMpred : Prediction of transmembrane regions and protein orientation (EMBnet-CH) + TopPred 2 : Topology prediction of membrane proteins (Stockholm University) |
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| Sequence Alignment Binary + Dotlet : A Java applet for sequence comparisons using the dot matrix method + LALIGN : Finds multiple matching subsegments in two sequences + SIM + LALNVIEW Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW Multiple + ALIGN : at Genestream (IGH) + AMAS : Analyse Multiply Aligned Sequences + Bork's alignment tools Various tools to enhance the results of multiple alignments (including consensus building) + CINEMA :Color Interactive Editor for Multiple Alignments + CLUSTALW + DIALIGN Multiple sequence alignment based on segment-to-segment comparison, at University of Bielefeld, Germany + ESPript : Tool to print a multiple alignment + Match-Box : at University of Namur, Belgium + MSA : at Washington University + Multalin + MUSCA : Multiple sequence alignment using pattern discovery, at IBM + Plogo : Sequence logos at CBS/Denmark + T-Coffee + WebLogo : Sequence logos at Cambridge/UK |
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