> Tag > Links tagged with 'algorithms'

Links tagged with 'algorithms'

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Found 370 links

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ChemMine ToolsTool Content

http://chemmine.ucr.edu [open in a new window]

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Other Molecules > Small Molecules

ChemMine Tools is an online service for analyzing and clustering small molecules. A suite of cheminformatics and data mining tools for data visualization, structure comparison, similarity searching, compound clustering and prediction of chemical properties are available.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
ChemMine tools: an online service for analyzing and clustering small molecules20116
NAR Web Server Issue 2011
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tagsalgorithms cluster analysis data mining drug discovery genomics pharmaceutical preparations small molecule libraries structure-activity relationship

ChimerDBDatabase Content

http://ercsb.ewha.ac.kr/fusiongene [open in a new window]

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DNA > Databases

ChimerDB is a knowledgebase of fusion genes identified from bioinformatics analysis of transcript sequences in the GenBank and various other public resources such as the Sanger cancer genome project (CGP), OMIM, PubMed and the Mitelman's database. A new algorithm that is more sensitive, has detected 2699 fusion transcripts with high confidence. Furthermore, it can identify interchromosomal translocations as well as the intrachromosomal deletions or inversions of large DNA segments. Results from the analysis of next-generation sequencing data in the short read archives are incorporated along with a new alignment viewer.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
ChimerDB 2.0--a knowledgebase for fusion genes updated20106
NAR Database Issue 2010
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external linksLink on Wikipedia
tagsalgorithms animals chromosomes computational biology expressed sequence tags gene expression profiling gene fusion genetic databases genetic translocation genomics humans information storage and retrieval internet messenger rna mice mutant chimeric proteins nucleic acid databases protein databases pubmed rats software user-computer interface

CHOPTool Content

https://rostlab.org/owiki/index.php/CHOPPER [open in a new window]

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Protein > Domains and Motifs
Sequence Comparison > Similarity Searching and Classification

CHOP takes a protein sequence as input, and returns a list of protein sequence fragments with homology to PDB and Pfam domains and to proteins from the SWISS-PROT database.

links directory index: 32
TitlePublication YearGoogle Scholar Citation Count
CHOP: parsing proteins into structural domains200432
NAR Web Server Issue 2004
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external linksLink on Twitter
tagsalgorithms amino acid sequence homology protein sequence analysis proteomics tertiary protein structure

CHpredictTool Content

http://www.imtech.res.in/raghava/chpredict [open in a new window]

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Protein > Biochemical Features
Protein > Networks & Interactions, Pathways and Enzymes

The CHpredict server predict two types of interactions: C-H...O and C-H...π interactions. For C-H...O interaction, the server predicts the residues whose backbone Cα atoms are involved in interaction with backbone oxygen atoms and for C-H...π interactions, it predicts the residues whose backbone Cα atoms are involved in interaction with π ring system of side chain aromatic moieties.

This content is being maintained by raghavagps.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Prediction of C alpha-H...O and C alpha-H...pi interactions in proteins using recurrent neural network20063
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tagsalgorithms alpha H O amino acid sequence ANN C alpha H pi computer simulation hydrogen bonding hydrogen bonding interactions molecular models molecular sequence data neural networks (computer) protein databases protein sequence analysis proteins secondary protein structure weak interactions

CLICKTool Content

http://mspc.bii.a-star.edu.sg/click [open in a new window]

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Protein > 3-D Structure Comparison

CLICK web server is a topology independent method of comparison of biomolecular 3D structures.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
CLICK--topology-independent comparison of biomolecular 3D structures20112
NAR Web Server Issue 2011
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tagsalgorithms molecular conformation molecular models nucleic acid conformation protein conformation rna

ClusProTool Content

http://cluspro.bu.edu/login.php [open in a new window]

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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.

links directory index: 511
TitlePublication YearGoogle Scholar Citation Count
Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19201033
PIPER: an FFT-based protein docking program with pairwise potentials2006100
ClusPro: an automated docking and discrimination method for the prediction of protein complexes2004247
ClusPro: a fully automated algorithm for protein-protein docking2004131
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

CMATool Content

http://www.gene-regulation.com/pub/programs/cma/CMA.html [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Composite Module Analyst (CMA) defines promoter models based on the composition of transcription factor binding sites (TFBS) in regulatory sequences for sets of coregulated genes.

links directory index: 66
TitlePublication YearGoogle Scholar Citation Count
Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm200623
Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations200643
NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence binding sites chemical models computer simulation dna sequence analysis endothelial cells gene expression profiling genetic promoter regions humans molecular sequence data protein binding protein sequence analysis transcription factors

CNVerTool Content

http://compbio.cs.toronto.edu/cnver/ [open in a new window]

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Human Genome > Sequence Polymorphisms
Sequence Comparison > Pairwise Sequence Alignments

CNVer is a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. CNVer combines this information within a unified computational framework called the donor graph, allowing it to better mitigate the sequencing biases that cause uneven local coverage.

links directory index: 23
TitlePublication YearGoogle Scholar Citation Count
Detecting copy number variation with mated short reads201023
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tagsalgorithms base pairing base sequence chromosome breakage chromosome mapping dna copy number variations dna mutational analysis dna shuffling high-throughput nucleotide sequencing humans reproducibility of results
setsUniversity of Toronto

Combinatorial Extension of the Optimal PathDatabase Content

http://cl.sdsc.edu/ce.html [open in a new window]

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Protein > 3-D Structure Comparison

Calculates structural alignments between two protein chains; or between a single chain and the entire Protein Data Bank.

links directory index: 1542
TitlePublication YearGoogle Scholar Citation Count
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path19981542
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tagsalgorithms amino acid sequence amino acid sequence homology molecular sequence data monte carlo method protein conformation protein folding proteins sequence alignment

CompareProspectorTool Content

http://compareprospector.stanford.edu/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.

links directory index: 164
TitlePublication YearGoogle Scholar Citation Count
A suite of web-based programs to search for transcriptional regulatory motifs200432
Eukaryotic regulatory element conservation analysis and identification using comparative genomics2004132
NAR Web Server Issue 2004
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tagsalgorithms animals binding sites caenorhabditis caenorhabditis elegans conserved sequence dna eukaryotic cells fungal genes gene expression regulation genes genetic transcription genomics helminth genes humans mice nucleic acid regulatory sequences regulator genes saccharomyces saccharomyces cerevisiae schizosaccharomyces transcription factors

CONREALTool Content

http://conreal.niob.knaw.nl/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.

links directory index: 125
TitlePublication YearGoogle Scholar Citation Count
CONREAL web server: identification and visualization of conserved transcription factor binding sites200541
CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting200484
NAR Web Server Issue 2005
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tagsalgorithms animals base sequence binding sites conserved sequence dna footprinting dna sequence analysis dna-binding proteins gene expression regulation genetic promoter regions hepatocyte nuclear factor 3-beta humans mice nuclear proteins nucleic acid regulatory sequences nucleic acid sequence homology phylogeny rats sequence alignment takifugu transcription factors zebrafish

Consensus ServerTool Content

http://ural.wustl.edu/consensus/ [open in a new window]

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Protein > 3-D Structure Comparison
Sequence Comparison > Comparative Genomics

The Consensus server aligns a sequence to a structural template using a consensus of 5 different alignment methods. A measure of reliability is produced for each alignment position in order to predict the suitability of regions for comparative modelling.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
Consensus alignment server for reliable comparative modeling with distant templates200411
NAR Web Server Issue 2004
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tagsalgorithms molecular models protein structural homology sequence alignment software validation

ConsiteTool Content

http://www.phylofoot.org/consite/ [open in a new window]

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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.

links directory index: 514
TitlePublication YearGoogle Scholar Citation Count
ConSite: web-based prediction of regulatory elements using cross-species comparison2004250
Identification of conserved regulatory elements by comparative genome analysis2003264
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

CorGenTool Content

http://corgen.molgen.mpg.de [open in a new window]

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DNA > Structure and Sequence Feature Detection

CorGenmeasures long-range correlations in DNA sequences and can generate random sequences with the same (or user-specified) correlation and composition parameters.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
CorGen--measuring and generating long-range correlations for DNA sequence analysis200611
NAR Web Server Issue 2006
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tagsalgorithms base composition computational biology cytosine dna sequence analysis genomics guanine humans sequence alignment statistical data interpretation

corRnaTool Content

http://corrna.cs.mcgill.ca [open in a new window]

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RNA > Functional RNAs

corRna is a web server for predicting the multiple point deleterious mutations in structural RNAs. Users can apply search heuristics to improve the quality of the predictions.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
corRna: a web server for predicting multiple-point deleterious mutations in structural RNAs.20111
NAR Web Server Issue 2011
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tagsalgorithms mutagenesis mutation nucleic acid conformation rna

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