> Tag > Links tagged with 'genetic databases'

Links tagged with 'genetic databases'

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Found 306 links

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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

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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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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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

Ensembl Drosophila Genome BrowserDatabase Content

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

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Model Organisms > Fly

Access to the Fly genome through the Ensembl user interface (both for visualisation and data mining).

links directory index: 865
TitlePublication YearGoogle Scholar Citation Count
The Ensembl genome database project.2002865
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tagscomputational biology database management systems dna sequence analysis genetic databases human genome humans systems integration

Ensembl Fugu Genome BrowserDatabase Content

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

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Model Organisms > Fish

Fugu Ensembl is a joint project between The IMCB and the EMBL - EBI to produce and maintain an automatic annotation of the Fugu Genome.

links directory index: 865
TitlePublication YearGoogle Scholar Citation Count
The Ensembl genome database project.2002865
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tagscomputational biology database management systems dna sequence analysis genetic databases human genome humans systems integration

Ensembl Human Genome BrowserDatabase Content

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

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Model Organisms > Other Vertebrates

Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes; uses NCBI assembly.

links directory index: 865
TitlePublication YearGoogle Scholar Citation Count
The Ensembl genome database project.2002865
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tagscomputational biology database management systems dna sequence analysis genetic databases human genome humans systems integration

Ensembl Mosquito Genome BrowserDatabase Content

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

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Model Organisms > Fly

This site presents the tenfold whole genome shotgun assembly of the PEST strain of anopheles gambiae, as prepared by The International Anopheles Genome project.

links directory index: 865
TitlePublication YearGoogle Scholar Citation Count
The Ensembl genome database project.2002865
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tagscomputational biology database management systems dna sequence analysis genetic databases human genome humans systems integration

Ensembl Mouse Genome BrowserDatabase Content

http://www.ensembl.org/Mus_musculus/index.html [open in a new window]

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Model Organisms > Mouse and Rat

Analysis of finished and draft mouse genomic clone sequences.

links directory index: 865
TitlePublication YearGoogle Scholar Citation Count
The Ensembl genome database project.2002865
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tagscomputational biology database management systems dna sequence analysis genetic databases human genome humans systems integration

Ensembl Rat Genome BrowserDatabase Content

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

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Model Organisms > Mouse and Rat

The Rat Genome project is an international collaboration to sequence the genome of the brown rat (Rattus norvegicus).

links directory index: 865
TitlePublication YearGoogle Scholar Citation Count
The Ensembl genome database project.2002865
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tagscomputational biology database management systems dna sequence analysis genetic databases human genome humans systems integration

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

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.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count
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tagsanimals automatic data processing computational biology gene expression profiling genetic databases genomics humans oligonucleotide array sequence analysis

eShadowTool Content

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

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

A tool for phylogenetic shadowing of multiple sequences from closely related species. This analyses of multiple sequence alignments can be used to predict putative functional elements.

links directory index: 64
TitlePublication YearGoogle Scholar Citation Count
eShadow: a tool for comparing closely related sequences200464
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tagsanimals computational biology conserved sequence exons genetic databases humans intergenic dna papio peptides proteins software design tertiary protein structure

ESTExplorerTool Content

http://estexplorer.biolinfo.org [open in a new window]

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DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Networks & Interactions, Pathways and Enzymes

ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.

links directory index: 166
TitlePublication YearGoogle Scholar Citation Count
ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform200750
A hitchhiker's guide to expressed sequence tag (EST) analysis2007116
NAR Web Server Issue 2007
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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis expressed sequence tags female genetic databases genomics haemonchus humans male nucleic acid databases oligonucleotide array sequence analysis programming languages untranslated regions

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