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Links tagged with 'time factors'

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Found 23 links

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AntiHunter 2.0Tool Content

http://bio.ifom-ieo-campus.it/antihunter

Expression > Gene Regulation
Expression > cDNA, EST, SAGE

AnitHunter 2.0 is a tool to detect potential EST antisense transcripts within a given genomic region from the analysis of BLAST output.

NAR Web Server Issue 2005
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tagsalgorithms antisense rna dna sequence analysis expressed sequence tags genetic databases sequence alignment time factors

AutoSNPdbTool Content

http://autosnpdb.qfab.org.au/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

SNPServer combines BLAST, cap3 and a SNP discovery module into a single pipeline for the discovery of SNPs in user submitted files or dynamically created assemblies.

NAR Web Server Issue 2005
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tagsdna sequence analysis sequence alignment single nucleotide polymorphism time factors

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

BTWTool Content

http://bioinformatics.bc.edu/clotelab/BTW/

Expression > Transcript Expression Analysis

Boltzmann Time Warping (BTW) computes time warping distances and Boltzmann\' pair probabilities for a given input gene expression time series. This tool helps to identify genes that may share similar expression patterns over time.

NAR Web Server Issue 2006
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tagsalgorithms gene expression profiling genomics humans sequence alignment time factors

CD-SearchDatabase Content

http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

CD-Search allows the user to search the Conserved Domain Database (CDD) for conserved structural and functional domains in a sequence of interest; links to 3-D structures where applicable.

NAR Web Server Issue 2004
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tagsamino acid sequence animals consensus sequence conserved sequence molecular models protein databases protein sequence analysis proteins sequence alignment tertiary protein structure time factors

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

Human Gene Mutation DatabaseDatabase Content

http://www.hgmd.cf.ac.uk/ac/index.php

Human Genome > Health and Disease

The Human Gene Mutation Database comprises various types of mutation within the coding regions of human nuclear genes causing inherited disease.

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tagsbase sequence database management systems dna mutational analysis dna sequence analysis genes genetic databases genetic polymorphism genomics human genome humans molecular sequence data mutation single nucleotide polymorphism time factors

Influenza Virus ResourcesResource Content

http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html

Model Organisms > Other Organisms

Influenza Virus Resource presents data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis and annotation. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses.

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tagsanimals genetic recombination genetic variation genome h3n2 subtype influenza a virus human influenza humans influenza a virus influenza vaccines influenza virus hemagglutinin glycoproteins molecular evolution mutagenesis mutation neuraminidase new york phylogeny public sector reassortant viruses sequence analysis time factors viral genes viral genome virus replication

MDscanTool Content

http://robotics.stanford.edu/~xsliu/MDscan/

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

Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.

This content is being maintained by brutlag.

NAR Web Server Issue 2004
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tagsalgorithms base sequence binding sites chromatin computational biology dna dna-binding proteins fungal genes gene expression regulation genetic transcription nucleic acid regulatory sequences oligonucleotide array sequence analysis precipitin tests protein binding response elements saccharomyces cerevisiae saccharomyces cerevisiae proteins sensitivity and specificity telomere telomere-binding proteins time factors transcription factors

MICheckTool Content

http://www.genoscope.cns.fr/agc/tools/micheck/

DNA > Annotations

MICheck (Microbial Genome Checker) allows the user to verify gene annotations in previously published microbial genomes.

NAR Web Server Issue 2005
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tagsbacterial genes bacterial genome genomics nucleic acid databases reproducibility of results time factors

MRSTool Content

http://mrs.cmbi.ru.nl/

DNA > Sequence Retrieval and Submission
Protein > 3-D Structure Retrieval/Viewing
Protein > Sequence Retrieval

MRS is a biological data retrieval system that can be accessed over the web, or installed and used locally. MRS indexes several flat-file data sets for searching, including EMBL nucleotide, UniProt, PDB and KEGG. Searches can be performed globally, or on one or more flat file fields per data set.

This content is being maintained by maarten.

NAR Web Server Issue 2005
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tagsgenetic databases nucleic acid databases protein databases time factors

ParAlignTool Content

http://www.paralign.org/

Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

ParAlign provides a service for sequence similarity searching powered by parallel computing technology. The two comparison algorithms used are Smith-Waterman and ParAlign (a heuristic method for sequence alignment).

NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence homology computational biology computing methodologies factual databases microcomputers nucleic acid databases nucleic acid sequence homology protein databases sensitivity and specificity sequence alignment time factors

PASTTool Content

http://past.in.tum.de/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

Polypeptide Angles Suffix Tree (PAST) provides methods for searching three-dimensional protein structures and identifying frequent common substructures (structural motifs) using an approach independent of the sequence of amino acids.

This content is being maintained by taeubig.

NAR Web Server Issue 2006
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tagsprotein conformation protein databases time factors

pdbFunTool Content

http://pdbfun.uniroma2.it/

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

pdbFun allows the user to search the PDB as a database of annotated residues. One can limit the search by annotations such as domains, binding sites, active sites, solvent exposure and residue type.

NAR Web Server Issue 2005
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tagsalgorithms amino acids protein conformation protein databases proteins systems integration time factors

PfoldTool Content

http://www.daimi.au.dk/~compbio/pfold

RNA > Structure Prediction, Visualization, and Design

The Pfold server takes an alignment of RNA sequences as input and predicts a common secondary structure.

NAR Web Server Issue 2003
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tagsalgorithms bacterial rna base sequence biological evolution catalytic rna computational biology computer simulation endoribonucleases molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid sequence homology probability reproducibility of results ribonuclease p rna rna sequence analysis sequence alignment stochastic processes time factors