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Links tagged with 'sensitivity and specificity'

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Found 45 links

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3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs

3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence animals automation binding sites computational biology computer simulation conserved sequence factual databases false negative reactions humans molecular models molecular structure programming languages protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins sensitivity and specificity sequence alignment src homology domains statistical models surface properties

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2008
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tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)

CAPwebTool Content

http://bioinfo.curie.fr/CAPweb/

Expression > Transcript Expression Analysis

CGH array Analysis Platform (CAPweb) is a tool for storing, analyzing and visualizing CGH-array data.

NAR Web Server Issue 2006
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tagsalgorithms chromosome breakage chromosome mapping computational biology dna dna mutational analysis dna sequence analysis gene dosage genetic models genetic variation genomics humans in situ hybridization oligonucleotide array sequence analysis reproducibility of results sensitivity and specificity statistical models stochastic processes urinary bladder neoplasms

CHAOS/DIALIGN WWW serverTool Content

http://dialign.gobics.de/chaos-dialign-submission

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Multiple Sequence Alignments

The CHAOS/DIALIGN WWW server is a multiple sequence alignment site which passes input sequences through CHAOS to create a list of local similarites. These similarities serve as anchor points, allowing DIALIGN to conduct global alignments faster. ABC can then be used for the interactive visualization of the alignment.

NAR Web Server Issue 2004NAR Web Server Issue 2005
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tagsalgorithms animals chickens computational biology dna sequence analysis genome genomics humans leukemia mice neoplasm dna neoplasm genes nucleic acid regulatory sequences rats sensitivity and specificity sequence alignment software validation stem cells tetraodontiformes zebrafish

ClusProTool Content

http://cluspro.bu.edu/login.php

Protein > Molecular Dynamics and Docking

ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties.

NAR Web Server Issue 2004
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tagsalgorithms antibodies antigens binding sites biological models chemical models cluster analysis computational biology discriminant analysis energy transfer enzyme inhibitors fourier analysis molecular dynamics simulation molecular models monte carlo method protein binding protein conformation protein interaction mapping protein multimerization proteins reproducibility of results sensitivity and specificity static electricity time factors

ClustalWTool Content

http://www.ebi.ac.uk/clustalw/

Sequence Comparison > Multiple Sequence Alignments

Standard multiple sequence alignment.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence globins molecular sequence data nucleic acids phylogeny protein sequence analysis proteins secondary protein structure sensitivity and specificity sequence alignment sequence analysis

COMPASSTool Content

http://prodata.swmed.edu/compass/compass.php

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.

NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsamino acid motifs amino acid sequence amino acid sequence homology capsid proteins clathrin computational biology mamastrovirus molecular evolution molecular models molecular sequence data protein conformation protein databases protein structural homology proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment statistical data interpretation statistics as topic tertiary protein structure trna methyltransferases

ConsiteTool Content

http://www.phylofoot.org/consite/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.

NAR Web Server Issue 2004
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tagsalgorithms animals binding sites computational biology conserved sequence dna dna footprinting dna sequence analysis genetic models human genome humans nucleic acid regulatory sequences phylogeny predictive value of tests regulator genes sensitivity and specificity sequence alignment transcription factors

CRPDatabase Content

http://fasta.bioch.virginia.edu/crp/

Protein > Domains and Motifs
Protein > Sequence Features

Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated.

NAR Web Server Issue 2003
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tagsamino acid sequence biochemistry dna sequence analysis humans molecular sequence data neoplasm proteins neural networks (computer) phosphoproteins phosphorylation phosphoserine phosphothreonine phosphotyrosine protein sequence analysis proteins radioactive tracers recombinant proteins sensitivity and specificity

DIALTool Content

http://caps.ncbs.res.in/DIAL/home.html

Protein > 3-D Structure Prediction
Protein > Domains and Motifs

DIAL (Domain Identification Algorithm) is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.

NAR Web Server Issue 2005
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tagsalgorithms amino acid motifs amino acid sequence amino acids aspartic acid endopeptidases calmodulin chemical models cluster analysis database management systems documentation factual databases hydroxymethylbilane synthase molecular models molecular sequence data molecular structure papain porins protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment tertiary protein structure x-ray crystallography

DIALIGNTool Content

http://bibiserv.techfak.uni-bielefeld.de/dialign/

Sequence Comparison > Multiple Sequence Alignments

Multiple alignment program which assembles a global sequence alignment from gap-free local pairwise alignments. This method could be especially useful when comparing large sequences that have only local similarities.

NAR Web Server Issue 2004
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tagsalgorithms amino acid sequence amino acid sequence homology animals chickens computational biology dna sequence analysis genome humans leukemia mice molecular sequence data neoplasm dna neoplasm genes nucleic acid regulatory sequences protein sequence analysis proteins rats sensitivity and specificity sequence alignment software validation stem cells tetraodontiformes zebrafish

DisEMBLTool Content

http://dis.embl.de/

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

A computational tool for prediction of disordered/unstructured regions within a protein sequence.

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tagscircular dichroism humans ligands magnetic resonance spectroscopy neural networks (computer) protein conformation proteins proteome sensitivity and specificity src homology domains statistics as topic temperature theoretical models ultraviolet rays x-ray crystallography

DSHIFTTool Content

http://www.chem.cuhk.edu.hk/DSHIFT/

DNA > Structure and Sequence Feature Detection

DSHIFT is a web server for predicting chemical shifts of DNA sequences in random coil form or double helical B-form.

NAR Web Server Issue 2007
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tagsalgorithms base sequence biomolecular nuclear magnetic resonance carbon computational biology computer simulation dna magnetic resonance spectroscopy molecular models molecular sequence data molecular structure nucleic acid conformation oligonucleotides phosphorus programming languages protons reproducibility of results sensitivity and specificity stochastic processes temperature

ENDEAVOURTool Content

http://www.esat.kuleuven.be/endeavour

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

ENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.

This content is being maintained by ltranche.

NAR Web Server Issue 2008
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tagsalgorithms animal models animals caenorhabditis elegans cell differentiation chromosome mapping computational biology drosophila melanogaster gene expression regulation genes genetic models genetic predisposition to disease humans mice rats roc curve sensitivity and specificity statistical models zebrafish