NAR Web Server Issue 2014

Found 82 links

Displaying 15 links

AIDATool Content

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AIDA: Ab Initio Domain Assembly Server attempts to find the best domain arrangements while maintaining chain connectivity. The server also supports structure assembly from sequence only and restraint-guided simulation producing a final assembly satisfying user-specified inter-domain distance restraints.

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AlignMeTool Content

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AlignMe (for Alignment of Membrane Proteins) can be used to examine detailed similarity between homologous proteins even if there is no notable sequence similarity. The predefined gap/weight sets have been optimized for membrane proteins, and so should be particularly useful for these difficult cases.

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Alignment-AnnotatorTool Content

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Alignment Annotator is a web service which annotates and renders sequence alignments using annotation services and the PDB. The annotated and colorized alignment can be downloaded as an interactive HTML file for web browsers.

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AlkemioTool Content

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Alkemio: association of chemicals with biomedical topics by text and data mining

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BiERappTool Content

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BierApp is a web-based interactive framework to assist in the prioritization of disease candidate genes in whole exome sequencing studies.

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BioMet Toolbox 2.0Tool Content

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BioMet Toolbox 2.0 is a web server for genome-wide analysis of metabolism and omics data. BioMet Toolbox exploits the capabilites of metabolic networks described in genome scale models using flux analysis and random sampling, and gene set analysis and basic microarray analysis, thereby providing an integrated analysis to identify coregulated subnetwork structures within the metabolic network and also for identifying statistically significant gene sets enabling biological interpretation.

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BiQ Analyzer HiModTool Content

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BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives

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CAD-scoreTool Content

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The CAD-score web server provides a contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

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CFM-IDTool Content

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CFM-ID (Competitive Fragmentation Modeling) is a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra data.

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CHOPCHOPTool Content

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CHOPCHOP is a web tool for selecting the optimum target sites for CRISPR/Cas9- or TALEN-directed mutagenesis. It can be run with three basic input options, or with additional advanced parameters. The basic input comprises: (i) a gene name, genomic coordinates or a pasted sequence (accepting RefSeq, ENSEMBL, FlyBase and WormBase gene IDs); (ii) a growing list of organisms (including human, mouse, zebrafish, etc.); and (iii) the choice between CRISPR/Cas9 or TALEN mode.

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COGNACTool Content

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COGNAC: a webserver for searching and annotating hydrogen bonded base interactions in RNA 3-dimensional structures.

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CopraRNA and IntaRNATool Content

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CopraRNA and IntaRNA webserver tools: CopraRNA is a tool for sRNA target prediction, while IntaRNA enables the prediction of RNA-RNA interactions.

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COUGERTool Content

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COUGER - CO-factors associated with Uniquely-bound GEnomic Regions. This webserver can be applied to any two sets of genomic regions bound by paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify putative co-factors that provide specificity to each TF.

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DDI-CPITool Content

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DDI-CPI, is a web server that predicts Drug-Drug Interactions through implementing the Chemical-Protein Interactome.

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deepToolsTool Content

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deepTools: a flexible platform for exploring deep-sequencing data based on the Galaxy platform.

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