> Tag > Links tagged with 'animals'

Links tagged with 'animals'

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E-RNAiTool Content

http://e-rnai.dkfz.de/ [open in a new window]

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DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Fly
Model Organisms > Other Organisms
Model Organisms > Yeast
RNA > Structure Prediction, Visualization, and Design

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

links directory index: 579
TitlePublication YearGoogle Scholar Citation Count
E-RNAi: a web application for the multi-species design of RNAi reagents--2010 update20104
E-RNAi: a web application to design optimized RNAi constructs200565
Genome-wide RNAi analysis of growth and viability in Drosophila cells2004510
NAR Web Server Issue 2005NAR Web Server Issue 2010
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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

EBI patent sequence databaseDatabase Content

http://www.ebi.ac.uk/patentdata/nr/ [open in a new window]

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DNA > Databases

The EBI Patent Sequence Database is a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Non-redundant patent sequence databases with value-added annotations at two levels20103
NAR Database Issue 2010
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tagsalgorithms animals biotechnology computational biology europe factual databases gene expression profiling genetic databases humans patents as topic protein databases
setsEuropean Bioinformatics Institute (EBI)

ECR BrowserTool Content

http://ecrbrowser.dcode.org/ [open in a new window]

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Model Organisms > Fish
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates
Sequence Comparison > Analysis of Aligned Sequences

The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the genomes represented.

links directory index: 222
TitlePublication YearGoogle Scholar Citation Count
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes2004222
NAR Web Server Issue 2004
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tagsanimals binding sites dna sequence analysis fishes genome genomics humans mice nucleic acid regulatory sequences rats sequence alignment synteny systems integration transcription factors

eggNOGDatabase Content

http://eggnog.embl.de/version_2/ [open in a new window]

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Protein > Databases

eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).s (built from 2,590,259 proteins) and provides a broad functional description for at least 1,966,709 (88%) of them.

links directory index: 79
TitlePublication YearGoogle Scholar Citation Count
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges20121
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations201078
NAR Database Issue 2010
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tagsamino acid motifs animals archaea bacterial genome computational biology fishes genetic databases humans nucleic acid databases primates protein databases rats tertiary protein structure

ElastoDBDatabase Content

http://www.compsysbio.org/elastin/ [open in a new window]

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Protein > Databases
Sequence Comparison > Comparative Genomics

ElastoDB is a repository for well-characterized elastin sequences to facilitate its study. The database has since expanded to include other non-elastin sequences that share elastic properties.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
Comparative genomics of elastin: Sequence analysis of a highly repetitive protein200711
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tagsamino acid sequence animals chickens elastin humans molecular evolution molecular sequence data phylogeny ranidae xenopus xenopus proteins zebrafish zebrafish proteins
setsUniversity of Toronto

ELMTool Content

http://elm.eu.org/ [open in a new window]

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Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.

links directory index: 1035
TitlePublication YearGoogle Scholar Citation Count
ELM--the database of eukaryotic linear motifs201215
ELM: the status of the 2010 eukaryotic linear motif resource201090
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
NAR Database Issue 2010NAR Web Server Issue 2003
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external linksLink on Wikipedia
tagsamino acid motifs amino acid sequence amino acid sequence homology animals computational biology computer graphics disease eukaryota eukaryotic cells genetic databases humans information storage and retrieval internet molecular sequence data nucleic acid databases protein databases protein sequence analysis proteins software tertiary protein structure user-computer interface viral proteins

EMAGEDatabase Content

http://www.emouseatlas.org/emage/ [open in a new window]

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Expression > Databases
Model Organisms > Databases

EMAGE is a freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages of development, which allows data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, which allows data to be queried using text-based methods. Data coverage has been increased by sourcing from a greater selection of journals.

links directory index: 30
TitlePublication YearGoogle Scholar Citation Count
The BioMart interface to the eMouseAtlas gene expression database EMAGE20112
EMAGE mouse embryo spatial gene expression database: 2010 update201028
NAR Database Issue 2010
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external linksLink on Wikipedia
tagsaccess to information animals automation computational biology database management systems developmental gene expression regulation embryonic development factual databases gene expression gene expression profiling genetic databases immunohistochemistry in situ hybridization information storage and retrieval internet mammalian embryo messenger rna mice molecular imaging nucleic acid databases programming languages proteins reporter genes software user-computer interface

EMMADatabase Content

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

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Model Organisms > Databases

The European Mouse Mutant Archive (EMMA) is an infrastructure for archiving and worldwide provision of mouse mutant strains. It operates in collaboration with the other members of the Federation of International Mouse Resources (FIMRe), EMMA being the European component. The EMMA database gathers and curates extensive data on each line and presents it through a user-friendly website. A BioMart interface allows advanced searching including integrated querying with other resources e.g. Ensembl.

This content is being maintained by damiansmedley.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
EMMA--mouse mutant resources for the international scientific community201014
NAR Database Issue 2010
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tagsanimals chromosomes computational biology genetic databases genetic models inbred c57bl mice knockout mice mice nucleic acid databases protein databases tertiary protein structure

ENCODE DCCDatabase Content

http://encodeproject.org/ENCODE/ [open in a new window]

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DNA > Databases
Expression > Databases
Protein > Databases
RNA > Databases

The ENCODE project has a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) serves as the central repository for ENCODE data. The DCC contains a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser. ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay.

links directory index: 122
TitlePublication YearGoogle Scholar Citation Count
ENCODE whole-genome data in the UCSC genome browser (2011 update)201136
ENCODE whole-genome data in the UCSC Genome Browser201086
NAR Database Issue 2010NAR Database Issue 2011
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tagsanimals computational biology gene expression regulation genetic databases genomics human genome humans mice nucleic acid databases sequence alignment tumor cell line

ENDEAVOURTool Content

http://www.esat.kuleuven.be/endeavour [open in a new window]

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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.

links directory index: 412
TitlePublication YearGoogle Scholar Citation Count
ENDEAVOUR update: a web resource for gene prioritization in multiple species200867
Gene prioritization through genomic data fusion2006345
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

ePMVTool Content

http://epmv.scripps.edu/ [open in a new window]

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Protein > 3-D Structure Retrieval/Viewing
Protein > Molecular Dynamics and Docking

We have developed an open-source plug-in, embedded Python Molecular Viewer (ePMV), that runs molecular modeling software directly inside of professional 3D animation applications (blender,maya and cinema4D) to provide simultaneous access the capabilities of all of the systems. Uniting host and scientific algorithms into a single interface allows users from varied backgrounds to assemble professional quality visuals and to perform computational experiments with relative ease.

This content is being maintained by ludovicautin.

links directory index: not available
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tags3D algorithms animals blender cinema4d computational biology computer graphics electrocardiography female fetal heart fetal monitoring fetus heart rate humans interdisciplinary communication maya mice modelling molecular biology molecular conformation molecular dynamics simulation molecular graphism molecular models motion movement phtorealistic pregnancy prospective studies rem sleep rendering software three-dimensional imaging user-computer interface vizualisation

EponineTool Content

http://www.sanger.ac.uk/resources/software/eponine/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Eponine is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent positional accuracy.

links directory index: 226
TitlePublication YearGoogle Scholar Citation Count
Computational detection and location of transcription start sites in mammalian genomic DNA2002226
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tagsanimals bayes theorem complementary dna computational biology dna genetic models genetic promoter regions genome human genome humans mice transcription initiation site

eProbalignTool Content

http://probalign.njit.edu/probalign/login [open in a new window]

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Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

eProbalign computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. eProbalign also provides a platform to visualize the alignment, generate images, and manipulate the output.

links directory index: 77
TitlePublication YearGoogle Scholar Citation Count
eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities20076
Probalign: multiple sequence alignment using partition function posterior probabilities200671
NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid sequence homology animals computational biology computer simulation dna genetic databases humans molecular sequence data probability protein sequence analysis sequence alignment software design statistical models temperature thermodynamics

ERANGETool Content

http://woldlab.caltech.edu/rnaseq/ [open in a new window]

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Expression > Gene Regulation

A package of python scripts designed to analyze ultra-high-througphut sequencing data from the Illumina/Solexa platform for RNA-seq and ChIP-seq in metazoan genomes. The RNA-seq portion of ERANGE is described in our Nature Methods paper "Mapping and quantifying mammalian transcriptomes by RNA-Seq" (Mortazavi, 2008). ERANGE is built on top of Cistematic.

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tags3' untranslated regions algorithms alternative splicing animals brain chromosome mapping exons gene expression profiling genetic promoter regions inbred c57bl mice liver messenger rna mice nucleic acid databases oligonucleotide array sequence analysis rna rna sequence analysis rna splicing sensitivity and specificity skeletal muscle software

ErmineJTool Content

http://chibi.ubc.ca/ermineJ [open in a new window]

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Expression > Gene Set Analysis

ErmineJ is software for the analysis of functionally interesting patterns in large gene lists drawn from gene expression profiling data or other high-throughput genomics studies. It can be used by biologists with no bioinformatics background to conduct sophisticated analyses of gene sets with multiple methods. It allows users to assess whether microarray data or other gene lists are enriched for a particular pathway or gene class.

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tagsanimals automatic data processing computational biology gene expression profiling genetic databases genomics humans oligonucleotide array sequence analysis

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