The table below contains links to all of the resources in the NAR 2006 Web Server Issue. To record your experience of a service, login to the wiki and write a few words in the “user comments” column. Use the formatting in that column as a guide.
| Service | Description | User comments |
|---|---|---|
| BLAST | Basic Local Alignment and Search Tool | - It works for me! Neil |
| FISH | family identification of sequence homologues using structure anchored hidden Markov models | none yet |
| MIGenAS | integrated bioinformatics toolkit for web-based sequence analysis | none yet |
| PreBI | prediction of biological interfaces of proteins in crystals | none yet |
| PAST | fast structure-based searching in the PDB | none yet |
| oGNM | computation of structural dynamics using the Gaussian Network Model | none yet |
| PDB_Hydro | incorporating dipolar solvents with variable density in the PoissonBoltzmann treatment of macromolecule electrostatics | none yet |
| PHEPS | web-based pH-dependent Protein Electrostatics Server | none yet |
| pKD | re-designing protein pKa values | none yet |
| NOMAD-Ref | visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis | none yet |
| UMMS | constrained harmonic and anharmonic analyses of macromolecules based on elastic network models | none yet |
| PREDITOR | a web server for predicting protein torsion angle restraints | none yet |
| FOLD-RATE | prediction of protein folding rates from amino acid sequence | none yet |
| Protein Peeling 2 | a web server to convert protein structures into series of protein units | none yet |
| ProSAT2 | Protein Structure Annotation Server | none yet |
| FeatureMap3D | a tool to map protein features and sequence conservation onto homologous structures in the PDB | none yet |
| ProKware | integrated software for presenting protein structural properties in protein tertiary structures | none yet |
| OPAAS | a web server for optimal, permuted, and other alternative alignments of protein structures | none yet |
| Localizome | a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information | none yet |
| TreeDomViewer | a tool for the visualization of phylogeny and protein domain structure | none yet |
| TreeDet | a web server to explore sequence space | I used an alignment of 188 sequences of SH3 domains and the server worked well on firefox. Results were sent by email (after a couple of hours) and apart from the visual output the user has access to XML files describing the results. I have no expertise to study the quality of the results. - Pedro |
| CASTp | computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues | none yet |
| Protein Block Expert | a web-based protein structure analysis server using a structural alphabet | none yet |
| ReadOut | structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition | none yet |
| 3dSS | 3D structural superposition | none yet |
| MAVL/StickWRLD | analyzing structural constraints using interpositional dependencies in biomolecular sequence alignments | none yet |
| HHrep | de novo protein repeat detection and the origin of TIM barrels | none yet |
| Cascade PSI-BLAST | a remote homology search tool for relating protein domains | none yet |
| SABBAC | Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace | none yet |
| (PS)2 | protein structure prediction server | none yet |
| KemaDom | domain prediction using kernel machine with local context | none yet |
| DISULFIND | a disulfide bonding state and cysteine connectivity prediction server | none yet |
| DiANNA 1.1 | an extension of the DiANNA web server for ternary cysteine classification | none yet |
| PROFtmb | predicting bacterial transmembrane beta barrel proteins | none yet |
| transFold | predicting the structure and residue contacts of transmembrane beta-barrels | none yet |
| SVMHC | prediction of MHC-binding peptides | none yet |
| REMUS | a tool for identification of unique peptide segments as epitopes | none yet |
| AlgPred | prediction of allergenic proteins and mapping of IgE epitopes | none yet |
| pTARGET | predicting protein subcellular localization | none yet |
| DOUTFinder | identification of distant domain outliers using subsignificant sequence similarity | none yet |
| TarFisDock | identifying drug targets with docking approach | none yet |
| sgTarget | a target selection resource for structural genomics | none yet |
| HARMONY | for the assessment of protein structures | none yet |
| Rosetta Design | RosettaDesign server for protein design | none yet |
| CUPSAT | prediction of protein stability upon point mutations | none yet |
| BindN | a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences | none yet |
| MeMo | for prediction of protein methylation modifications | none yet |
| SUMOsp | for sumoylation site prediction | I tried this with 8 proteins known to be SUMOylated and with their stringent cut-off 7 of them are marked with at least one sumoylation site. The strange thing was that I also took around 15 random proteins from the human genome and 12 of them were also marked with at least one site with the same cut-off. I might send them an email about it. - Pedro |
| MODi | identifying multiple post-translational peptide modifications from tandem mass spectra | none yet |
| DyNAVacS | an integrative tool for optimized DNA vaccine design | none yet |
| NeuroPred | a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides | none yet |
| BAGEL | a web-based bacteriocin genome mining tool | none yet |
| GeneAlign | a coding exon prediction tool based on phylogenetical comparisons | none yet |
| TOM | a web-based integrated approach for identification of candidate disease genes | Came up with at least one plausible candidate gene in the region I searched, so it works. Frankly, though, if you were coming to this sort of thing cold you'd be lost: the UI needs some work (and so does the help: what the hell is a GO histogram in this context?) - Stew |
| WEGO | a web tool for plotting GO annotations | none yet |
| APID | Agile Protein Interaction DataAnalyzer | none yet |
| Protemot | prediction of protein binding sites with automatically extracted geometrical templates | none yet |
| GRAMM-X | for proteinprotein docking | Submitted job took several days and failed. Returned log files were uninformative. -Neil |
| TSEMA | interactive prediction of protein pairings between interacting families | none yet |
| kinDOCK | a tool for comparative docking of protein kinase ligands | none yet |
| YOGY | a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms | none yet |
| MPI Bioinformatics Toolkit | for protein sequence analysis | A very clean and useful set of advanced tools for sequence analysis and remote homology detection. The web interface is one of the best I've used for bioinformatics tools (Firefox/Opera friendly and complete with “Web 2.0” colour scheme :) ). As well as the usual BLAST, PSI-BLAST and secondary structure prediction methods, there are some powerful new tools such as HHpred and HHsenser, which use HMM-HMM comparisons to find and verify distant homologs, ultimately returning more useful hits than a single PSI-BLAST search. The MPI Toolkit is a good rival to the NCBI and ExPASy web based tools, but with the nicer web interface, some direct integration between inputs/outputs of tools and better job managment, it has fast become my favorite. – Andrew |
| VIRGO | computational prediction of gene functions | none yet |
| TACT | Transcriptome Auto-annotation Conducting Tool of H-InvDB | none yet |
| DILIMOT | discovery of linear motifs in proteins | none yet |
| MAGIIC-PRO | detecting functional signatures by efficient discovery of long patterns in protein sequences | none yet |
| ScanProsite | detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins | none yet |
| MicroFootPrinter | a tool for phylogenetic footprinting in prokaryotic genomes | none yet |
| MEME | discovering and analyzing DNA and protein sequence motifs | none yet |
| HHsenser | exhaustive transitive profile search using HMMHMM comparison | none yet |
| JAFA | a protein function annotation meta-server | none yet |
| SWAKK | for detecting positive selection in proteins using a sliding window substitution rate analysis | none yet |
| Virtual Ribosome | a comprehensive DNA translation tool with support for integration of sequence feature annotation | none yet |
| GenDecoder | genetic code prediction for metazoan mitochondria | none yet |
| NAST | a multiple sequence alignment server for comparative analysis of 16S rRNA genes | none yet |
| CrossLink | visualization and exploration of sequence relationships between (micro) RNAs | none yet |
| CorreLogo | an online server for 3D sequence logos of RNA and DNA alignments | none yet |
| ARTS | for aligning RNA tertiary structures | none yet |
| PseudoViewer | web application and web service for visualizing RNA pseudoknots and secondary structures | none yet |
| RNAMST | efficient and flexible approach for identifying RNA structural homologs | none yet |
| RegRNA | an integrated web server for identifying regulatory RNA motifs and elements | none yet |
| AUGUSTUS | ab initio prediction of alternative transcripts | none yet |
| ASPIC | a web resource for alternative splicing prediction and transcript isoforms characterization | none yet |
| ASGS | an alternative splicing graph web service | none yet |
| siVirus | web-based antiviral siRNA design software for highly divergent viral sequences | none yet |
| RNAhybrid | microRNA target prediction easy, fast and flexible | none yet |
| ProMiR II | a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs | none yet |
| EGassembler | for large-scale processing, clustering and assembling ESTs and genomic DNA fragments | none yet |
| jpHMM at GOBICS | a web server to detect genomic recombinations in HIV-1 | none yet |
| BiologicalNetworks | visualization and analysis tool for systems biology | none yet |
| BABELOMICS | a systems biology perspective in the functional annotation of genome-scale experiments | none yet |
| CAPweb | a bioinformatics CGH array Analysis Platform | none yet |
| BTW | a web server for Boltzmann time warping of gene expression time series | none yet |
| GEPAS | Next station in microarray data analysis | none yet |
| GEPS | the Gene Expression Pattern Scanner | none yet |
| CARMAweb | comprehensive R- and bioconductor-based web service for microarray data analysis | none yet |
| Arabidopsis Co-expression Tool (ACT) | for microarray-based gene expression analysis | none yet |
| JProGO | a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information | none yet |
| Zinc Finger Tools | custom DNA-binding domains for transcription factors and nucleases | none yet |
| TFBScluster web server | for the identification of mammalian composite regulatory elements | none yet |
| VOMBAT | prediction of transcription factor binding sites using variable order Bayesian trees | none yet |
| POXO | a web-enabled tool series to discover transcription factor binding sites | none yet |
| Composite Module Analyst | identification of transcription factor binding site combinations using genetic algorithm | Worked on random sequences. When I tried something else, got: “Exception: /www/gene/cgi-bin/CMA/prfs/pituitary_specific.prf: Cannot open file” Max |
| jPREdictor | a versatile tool for the prediction of cis-regulatory elements | none yet |
| CEAS | cis-regulatory element annotation system | none yet |
| Stubb | a program for discovery and analysis of cis-regulatory modules | none yet |
| NXSensor | for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors | none yet |
| MoD Tools | regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes | Offline? (23.7.06), max Redirects to this page (27.07.06) - Neil |
| CRSD | for composite regulatory signature discovery | none yet |
| PromAn | an integrated knowledge-based web server dedicated to promoter analysis | none yet |
| iCR | a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species | none yet |
| TICO | for postprocessing the predictions of prokaryotic translation initiation sites | none yet |
| FeatureScan | revealing property-dependent similarity of nucleotide sequences | none yet |
| Kalign, Kalignvu and Mumsa | web servers for multiple sequence alignment | none yet |
| PROTOGENE | turning amino acid alignments into bona fide CDS nucleotide alignments | Tried with same 7 AA sequences as for PAL2NAL. These were kin-1 sequences from 7 different nematode species - Protogene came back with 13 splice variants of the C.elegans kin-1, three C. elegans genomic seqs to do with kin-1 and a single C. briggsae CDS and aligned these. SAB |
| Expresso | automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee | none yet |
| PAL2NAL | robust conversion of protein sequence alignments into the corresponding codon alignments | Should accept same format as EMBOSS' 'tranalign'. Tried with 7 aligned AA sequences in .aln and corresponding nucleotides in .tfa - tranalign aligns 6 of 7, PAL2NAL outputs AA and corresponding nuc sequence of 1 of 7 entries, no alignment. SAB |
| AliWABA | alignment on the web through an A-Bruijn approach | none yet |
| FootPrinter3 | phylogenetic footprinting in partially alignable sequences | none yet |
| PupaSuite | finding functional single nucleotide polymorphisms for large-scale genotyping purposes | none yet |
| New Onto-Tools | Promoter-Express, nsSNPCounter and Onto-Translate | none yet |
| PDA v.2 | improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA | none yet |
| FASTSNP | an always up-to-date and extendable service for SNP function analysis and prioritization | none yet |
| SNP@Domain | a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences | none yet |
| Applications for protein sequence-function evolution data | mRNA/protein expression analysis and coding SNP scoring tools | none yet |
| SNPmasker | automatic masking of SNPs and repeats across eukaryotic genomes | none yet |
| SSRPrimer and SSR Taxonomy Tree | Biome SSR discovery | none yet |
| MutScreener | primer design tool for PCR-direct sequencing | none yet |
| PrimerStation | a highly specific multiplex genomic PCR primer design server for the human genome | none yet |
| GeMprospector | online design of cross-species genetic marker candidates in legumes and grasses | none yet |
| QGRS Mapper | a web-based server for predicting G-quadruplexes in nucleotide sequences | none yet |
| Quadfinder | for identification and analysis of quadruplex-forming motifs in nucleotide sequences | none yet |
| GC-Profile | a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences | none yet |
| CorGen | measuring and generating long-range correlations for DNA sequence analysis | none yet |
| SPRING | for the analysis of genome rearrangement using reversals and block-interchanges | none yet |
| ModelTest Server | for the statistical selection of models of nucleotide substitution online | none yet |
| The internal transcribed spacer 2 database | for (not only) low level phylogenetic analyses | none yet |
| PLOTREP | for defragmentation and visual analysis of dispersed genomic repeats | none yet |
| Path-A | metabolic pathway prediction web server | The server worked well on Firefox1.5. I submitted a small mycoplasma proteome for analysis and browsed around the results easily. A big drawback of the service was that I could not find a way to download the results after processing.- Pedro |
| KOBAS server | a web-based platform for automated annotation and pathway identification | none yet |
| metaSHARK | a WWW platform for interactive exploration of metabolic networks | Java applet crashed my browser (Firefox 1.5, Ubuntu 6.06) - Neil The applet also crashes on XP with IE7 and it hangs on XP with Firefox1.5 - Pedro Hangs on Mac OS X Tiger with Firefox 2.0, too - Stew |
| Taverna | for building and running workflows of services | none yet |
| GlyNest and CASPER | two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interface | none yet |
| FAF-Drugs | free ADME/tox filtering of compound collections | none yet |
| HubMed | a web-based biomedical literature search interface | none yet |
| botXminer | mining biomedical literature with a new web-based application | none yet |