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Links tagged with 'predictive value of tests'

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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

Gene Expression Data AnalyzerTool Content

http://bioinformatics.upmc.edu/GE2/GEDA.html

Expression > Transcript Expression Analysis

The Gene Expression Data Analyzer (GEDA) is a tool for discovering differential gene expression in a subset of patients. It is tailored to cancer-related microarray studies and offers extensive options for visualization, classification and normalization.

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tagsacute disease algorithms artificial intelligence classification cluster analysis gene expression profiling genes human genome humans myeloid leukemia neoplastic gene expression regulation oligonucleotide array sequence analysis predictive value of tests reference standards treatment failure treatment outcome

PANTHER ToolsTool Content

http://www.pantherdb.org/tools/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis
Human Genome > Annotations
Human Genome > Sequence Polymorphisms
Model Organisms > Fly
Model Organisms > Mouse and Rat
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function. The PANTHER research tools allow you to score proteins against the PANTHER HMM library, use PANTHER to do gene expression analyses, and download PANTHER tools and data.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence animals biological evolution computational biology database management systems gene expression profiling genetic variation humans inborn genetic diseases markov chains mice missense mutation peptide library phylogeny predictive value of tests protein databases protein sequence analysis proteins rats sequence alignment signal transduction single nucleotide polymorphism systems integration terminology as topic tertiary protein structure

PipeAlignTool Content

http://bips.u-strasbg.fr/PipeAlign/

Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

PipeAlign takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial proteins caenorhabditis elegans cluster analysis computational biology conserved sequence cytoplasmic and nuclear receptors factual databases fungal proteins gene expression profiling genetic transcription genomics haemophilus influenzae humans leukemia molecular sequence data phylogeny predictive value of tests protein databases protein sequence analysis proteins pyrococcus reproducibility of results saccharomyces cerevisiae sensitivity and specificity sequence alignment small nuclear ribonucleoproteins

pknotsRGTool Content

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

RNA > Structure Prediction, Visualization, and Design

pknotsRG is a server for single sequence RNA secondary structure prediction including pseudoknots; source code, binary executable, and web service available.

NAR Web Server Issue 2007
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tagsalgorithms computational biology computer simulation genetic models hepatitis delta virus nucleic acid conformation predictive value of tests programming languages rna statistical models thermodynamics viral rna

PRED-TMBBTool Content

http://bioinformatics.biol.uoa.gr/PRED-TMBB/

Protein > 2-D Structure Prediction
Protein > Localization and Targeting

PRED-TMBB is a tool that takes a Gram-negative bacteria protein sequence as input and predicts the transmembrane strands and the probability of it being an outer membrane beta-barrel protein. The user has a choice of three different decoding methods.

This content is being maintained by pbagos.

NAR Web Server Issue 2004
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tagsbacterial outer membrane proteins escherichia coli proteins gram-negative bacteria hidden markov model markov chains membrane proteins peptides predictive value of tests protein databases protein sequence analysis secondary protein structure statistical models tertiary protein structure topology prediction

RNABindRTool Content

http://bindr.gdcb.iastate.edu/RNABindR/

Protein > Domains and Motifs

RNABindR is a server for analyzing and predicting RNA binding sites in proteins.

NAR Web Server Issue 2007
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tagsamino acid motifs amino acid sequence amino acids animals artificial intelligence bayes theorem binding sites computational biology humans molecular models molecular sequence data predictive value of tests protein conformation protein databases protein sequence analysis proteins reproducibility of results rna sensitivity and specificity

SCOPETool Content

http://genie.dartmouth.edu/scope/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

SCOPE (Suite for Computational identification Of Promoter Elements) is a set of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences. SCOPE does not have any nuisance parameters so does not require the user to guess what the results might be. SCOPE is also very robust to noisy data and is still 50% as accurate even in the presence of 4-fold noise. SCOPE can also identify other genes in the genome that might be coregulated with the original gene set.

This content is being maintained by bobgross.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence homology artificial intelligence automated pattern recognition base sequence binding sites cluster analysis computational biology computer simulation consensus sequence conserved sequence dna dna sequence analysis gene expression profiling gene expression regulation genetic models genetic promoter regions molecular sequence data oligonucleotide array sequence analysis predictive value of tests protein binding proteins response elements saccharomyces cerevisiae sequence alignment statistical models transcription factors transcriptional regulatory elements

SVMHCTool Content

http://www-abi.informatik.uni-tuebingen.de/Services/SVMHC/

DNA > Sequence Polymorphisms
Human Genome > Other Resources
Human Genome > Sequence Polymorphisms
Protein > Interactions, Pathways, Enzymes

SVMHC is a server for prediction of MHC class I and class II binding peptides. SVMHC can be used to find likely binders in a protein sequence and to investigate the effects of single nucleotide polymorphisms on MHC-peptide binding.

NAR Web Server Issue 2006
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tagsalleles animals artificial intelligence computational biology histocompatibility antigens histocompatibility antigens class i hla antigens humans mice peptides predictive value of tests protein binding protein databases protein sequence analysis sensitivity and specificity single nucleotide polymorphism t-lymphocyte epitopes

TwinscanTool Content

http://genes.cs.wustl.edu/

DNA > Gene Prediction

Twinscan is a system for predicting gene-structure in eukaryotic genomic sequences. In order to make its predictions, Twinscan combines the information from predicted coding regions and splice sites with conserservation measurements between the target sequence and sequences from a closely related genome. Currently sequences from mammalian genomes, and those of Arabidopsis thaliana, C. elegans, C. briggsae and strains JEC21 and H99 of Cryptococcus neoformans can be processed using Twinscan.

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tagsalgorithms animals base composition base sequence chromosome mapping computational biology conserved sequence dna exons forecasting gc rich sequence genes genome human genome humans mice molecular evolution nucleic acid sequence homology predictive value of tests sensitivity and specificity sequence alignment statistical models synteny