Meta sites for DNA & protein analyses
Sites which permit one to carry out a variety of analyses include:
EMBOSS
EMBOSS (European Molecular Biology Open Source Software Suite) can be accessed here (SourceForge, U.S.A.). A list of their programs is appended. Some of these tools can also be accessed at the EMBL-EBI site.
SeWeR
SeWeR (SEquence analysis using WEb Resources) from The Bioinformatics Organization, MBIdeas Innovation Center, U.S.A., is also a Java suite for analyzing nucleic acids and proteins.
The Biology WorkBench
The Biology WorkBench (San Diego Supercomputing Center, University of California San Diego, U.S.A.). No longer funded.
Sequence Manipulation Suite
Sequence Manipulation Suite or here (Bioinformatics.org).
SCRATCH Protein Predictor
SCRATCH Protein Predictor (Institute for Genomics and Bioinformatics, University of California, Irvine, USA) includes ACCpro: Solvent Accessibility; ACCpro20: Solvent Accessibility (20 Class); SSpro: Secondary Structure (3 Class); SSpro8: Secondary Structure (8 Class); DISpro: Disorder; CONpro: Contact Number; CMAPpro: Contact Map; SVMcon: New SVM Contact Map; 3Dpro: Tertiary Structure; DOMpro: Domains; DIpro: Disulfide Bonds; SOLpro: Solubility upon Overexpression; and COBEpro: Continuous B-cell Epitopes.
PSIPRED Protein Sequence Analysis Workbench
PSIPRED Protein Sequence Analysis Workbench
includes PSIPRED v3.3 (Predict Secondary Structure); DISOPRED3 and
DISOPRED2 (Disorder Prediction); pGenTHREADER (Profile Based Fold
Recognition); MEMSAT3 and MEMSAT-SVM (Membrane Helix Prediction);
BioSerf v2.0 (Automated Homology Modelling); DomPred (Protein Domain
Prediction); FFPred 3 (Eukaryotic Function Prediction); GenTHREADER
(Rapid Fold Recognition); MEMPACK (SVM Prediction of TM Topology and
Helix Packing); pDomTHREADER (Fold Domain Recognition); and DomSerf
v2.0 (Automated Domain Modelling by Homology).
(Reference: Buchan DWA et al. 2013. Nucl. Acids Res.
41(W1): W340-W348).
Rtools
Rtools (Computational Biology Research Consortium, Japan) is a bioinformatics web server for RNA (single FASTA format, <= 400 nt). In order to visualize the whole picture of the distribution of the secondary structure, this web server provides users with rich information on single RNA sequences using seven tools: (a) CentroidFold, based on a generalized centroid estimator, for RNA secondary structure prediction; (b) CentroidHomfold for RNA secondary structure prediction using automatically collected homologous sequences of the target; (c) IPknot for RNA secondary structures including a wide class of pseudoknots; (d) Rchange for entropy and internal energy changes of secondary structures for single-point mutated sequences; (e) CapR for calculating probabilities that each RNA base position is located within each secondary structural context for long RNA sequences; (f) Raccess for computing accessibility of a segment [a, b] = [x, x+l-1] in the transcript for all positions x with fixed length l (Acc.len = 5, 10, 20); and (g) RintD for validating RNA secondary structures. Target secondary structures are predicted by CentroidFold (inference engine: McCaskill) and RNAfold (minimum free energy structure).
ProteinsPlus
ProteinsPlus
offers a wide selection of tools, including PoseView and PoseEdit (2D
interaction diagrams), EDIA and StructureProfiler (X-ray structure
quality), LifeSoaks (X-ray solvent channels), METALizer (metal
coordination geometry), SIENA (binding site similarity), MicroMiner
(single residue mutations), ActivityFinder (ChEMBL compound activities),
GeoMine (geometrical site mining), Protoss (protonation state and
hydrogen atom position assignment), WarPP (water molecule placement),
DoGSite3 (binding site prediction), DoGSiteScorer (druggability
prediction), JAMDA (small molecule docking), and HyPPI (PPI
classification), to facilitate structure-based design. Users can use PDB
structures, predicted structures from the AlphaFold Protein Structure
Database, or individual structures (with or without ligands) for
analysis and prediction tasks.
(Reference: Ehrt C et al. 2025. Nucleic Acids Research
53(W1): W478-W484).
Updated: February, 2026