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Links tagged with 'humans'

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Found 482 links

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AREsiteDatabase Content

http://rna.tbi.univie.ac.at/AREsite [open in a new window]

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RNA > Databases

AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3'-untranslated regions (UTRs). AREsite allows one to quantify the structuredness of ARE motif sites in terms of opening energies and accessibility probabilities. A detailed phylogenetic analysis of ARE motifs and incorporate information about experimentally validated targets of the ARE-binding proteins TTP, HuR and Auf1 is also provided.

links directory index: 13
TitlePublication YearGoogle Scholar Citation Count
AREsite: a database for the comprehensive investigation of AU-rich elements201113
NAR Database Issue 2011
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external linksLink on Wikipedia
tags3' untranslated regions adenine animals base sequence conserved sequence genomics humans mice nucleic acid databases rna sequence analysis rna-binding proteins sequence alignment uracil

Argonne National Laboratory - Computational Biology DatabasesTool Content

http://www-unix.mcs.anl.gov/compbio/index.html [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

Provides several tools including WIT2, EMP, MPW, SENTRA and PatScan; other tools are also available.

links directory index: 833
TitlePublication YearGoogle Scholar Citation Count
Sentra, a database of signal transduction proteins200216
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction2000369
MPW: the Metabolic Pathways Database1998127
Searching for patterns in genomic data1997221
The metabolic pathway collection from EMP: the enzymes and metabolic pathways database1996100
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tagsanimals bacteria biological transport chemotaxis conserved sequence enzymes eukaryota factual databases fungi genome humans metabolism methylation multigene family open reading frames phosphorylation prokaryotic cells protein databases protein kinases protein-serine-threonine kinases proteins sequence homology signal transduction systems integration tertiary protein structure

ArrayProspectorTool Content

http://string32.embl-heidelberg.de:8080/prophecies_html/prophecies.html [open in a new window]

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Expression > Transcript Expression Analysis

ArrayProspector is a set of predicted functional associations between genes that have been inferred from microarray expression data from the Standford Microarray Database. Users can search for genes linked to query or for links between two genes.

links directory index: 21
TitlePublication YearGoogle Scholar Citation Count
ArrayProspector: a web resource of functional associations inferred from microarray expression data200421
NAR Web Server Issue 2004
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tagsalgorithms animals gene expression profiling humans oligonucleotide array sequence analysis proteins reproducibility of results

ArrayTrackTool Content

http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/ [open in a new window]

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Expression > Transcript Expression Analysis

ArrayTrack™ provides an integrated solution for managing, analyzing, and interpreting microarray gene expression data. Specifically, ArrayTrack™ is MIAME (Minimum Information About A Microarray Experiment)-supportive for storing both microarray data and experiment parameters associated with a pharmacogenomics or toxicogenomics study.

links directory index: 132
TitlePublication YearGoogle Scholar Citation Count
ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research2003132
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tagsfactual databases gene library humans oligonucleotide array sequence analysis protein array analysis public health informatics public sector reference values statistics as topic toxicogenetics toxicology united states united states food and drug administration

ASePCRTool Content

http://genome.ewha.ac.kr/ASePCR/ [open in a new window]

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DNA > Tools For the Bench
Expression > Splicing

ASePCR (Alternative Splicing electronic PCR) is a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
ASePCR: alternative splicing electronic RT-PCR in multiple tissues and organs200510
NAR Web Server Issue 2005
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tagsalgorithms alternative splicing animals base sequence expressed sequence tags humans messenger rna mice molecular sequence data rats reverse transcriptase polymerase chain reaction tissue distribution

ASmodelerTool Content

http://genome.ewha.ac.kr/ECgene/ASmodeler/ [open in a new window]

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Expression > Splicing
Model Organisms > Mouse and Rat
Sequence Comparison > Analysis of Aligned Sequences

Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences200424
NAR Web Server Issue 2004
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tagsalgorithms alternative splicing animals exons expressed sequence tags genetic models genome humans messenger rna mice molecular sequence data protein sequence analysis rats rna sequence analysis sequence alignment

ASPicDBDatabase Content

http://www.caspur.it/ASPicDB/ [open in a new window]

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Human Genome > Databases
Protein > Databases

ASPicDB provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256,939 protein variants from 17,191 multi-exon genes have been extensively annotated through machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user.

This content is being maintained by Graziano Pesole.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing20113
NAR Database Issue 2011
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tagsalternative splicing exons genetic databases genetic variation humans messenger rna protein isoforms protein sequence analysis proteins

AStalavistaTool Content

http://genome.imim.es/astalavista/ [open in a new window]

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Expression > Splicing

AStalavista (alternative splicing transcriptional landscape visualization tool) dynamically identifies, extracts, and displays alternative splicing events from whole genome annotations and user provided gene sets.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets200716
NAR Web Server Issue 2007
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tagsalternative splicing chromosome mapping computational biology dna probes dna sequence analysis genetic databases genome humans messenger rna oligonucleotide array sequence analysis rna splice sites

AsteriasTool Content

http://asterias.bioinfo.cnio.es/ [open in a new window]

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DNA > Annotations
Expression > Transcript Expression Analysis

Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.

This content is being maintained by rdiaz02.

links directory index: 555
TitlePublication YearGoogle Scholar Citation Count
Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite200713
Gene selection and classification of microarray data using random forest2006485
DNMAD: web-based diagnosis and normalization for microarray data200457
NAR Web Server Issue 2007
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tagsalgorithms animals automated pattern recognition automation cluster analysis computational biology computer simulation database management systems dna sequence analysis gene expression profiling genetic models genomics humans nucleic acid hybridization oligonucleotide array sequence analysis programming languages sequence alignment statistical models

ATIVSTool Content

http://influenza.nhri.org.tw/ATIVS/ [open in a new window]

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Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

ATIVS (analytical tool for influenza virus surveillance) is a web server for analyzing serological data of all influenza viruses and provide interpretive summaries. ATIVS also compares the HA1 sequences of viruses to those of the reference vaccine strains to predict influenza A/H3N2 antigenic drift.

This content is being maintained by Jade.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
ATIVS: analytical tool for influenza virus surveillance20094
NAR Web Server Issue 2009
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tagsantigenic variation h3n2 subtype influenza a virus human influenza humans influenza virus hemagglutinin glycoproteins orthomyxoviridae population surveillance sequence analysis viral antibodies viral antigens

AUGUSTUSTool Content

http://bioinf.uni-greifswald.de/augustus [open in a new window]

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DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Splicing
Protein > Domains and Motifs

AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.

This content is being maintained by Mario Stanke.

links directory index: 233
TitlePublication YearGoogle Scholar Citation Count
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources200687
AUGUSTUS: ab initio prediction of alternative transcripts200650
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints200534
AUGUSTUS: a web server for gene finding in eukaryotes200461
The formation of deoxycholic acid in patients with type II and IV hyperlipoproteinaemia19761
NAR Web Server Issue 2004NAR Web Server Issue 2005NAR Web Server Issue 2006
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tagsadult algorithms alternative splicing animals artificial intelligence automated pattern recognition base sequence bile acids and salts cholic acids chromosome mapping computer simulation deoxycholic acid dna sequence analysis drosophila melanogaster exons female gene components gene expression genes genetic databases genetic models genetic variation genomics human genome humans hypercholesterolemia hyperlipidemias introns ldl lipoproteins male markov chains middle aged molecular sequence data proteins sequence alignment statistical models stochastic processes triglycerides vldl lipoproteins

BCM Search LauncherResource Content

http://searchlauncher.bcm.tmc.edu/ [open in a new window]

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DNA > DNA and Genomic Analysis
Protein > Do-it-all Tools for Protein

Molecular biology-related search and analysis services organized by function; single point-of-entry for related searches (e.g., a single page for launching protein sequence searches using standard parameters).

links directory index: 355
TitlePublication YearGoogle Scholar Citation Count
BCM Search Launcher--an integrated interface to molecular biology data base search and analysis services available on the World Wide Web1996355
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tagsanimals database management systems factual databases humans molecular biology

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/ [open in a new window]

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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.

This content is being maintained by kimmen.

links directory index: 4963
TitlePublication YearGoogle Scholar Citation Count
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis200720
MUSCLE: multiple sequence alignment with high accuracy and high throughput20044855
SATCHMO: sequence alignment and tree construction using hidden Markov models200388
Phylogenetic inference in protein superfamilies: analysis of SH2 domains.19980
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

BIND - The Biomolecular Interaction Network DatabaseDatabase Content

http://bond.unleashedinformatics.com/Action [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records.

links directory index: 932
TitlePublication YearGoogle Scholar Citation Count
BIND: the Biomolecular Interaction Network Database2003752
BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways2000180
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tagsamino acid sequence animals dna factual databases humans macromolecular substances molecular biology protein databases protein interaction mapping proteins rna sequence alignment statistical models tertiary protein structure

BINDTranslationDatabase Content

http://download.baderlab.org/BINDTranslation/ [open in a new window]

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Expression > Networks
Other Molecules > Databases
Protein > Databases

Biomolecular Interaction Network Database (BIND): a database of curated biomolecular interactions.

This content is being maintained by baderg.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
The Biomolecular Interaction Network Database in PSI-MI 2.520115
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tagsanimals controlled vocabulary humans protein binding protein databases proteomics rats reproducibility of results
setsUniversity of Toronto

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