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Links tagged with 'genomics'

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AgBaseDatabase Content

http://www.agbase.msstate.edu/ [open in a new window]

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Model Organisms > Databases

AgBase provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
AgBase: supporting functional modeling in agricultural organisms20116
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsagricultural crops agriculture animals cats dogs domestic animals gene expression profiling genetic databases genetic models genomics oligonucleotide array sequence analysis

AGenDATool Content

http://bibiserv.techfak.uni-bielefeld.de/agenda/ [open in a new window]

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DNA > Gene Prediction
Sequence Comparison > Analysis of Aligned Sequences

AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
AGenDA: gene prediction by cross-species sequence comparison200411
NAR Web Server Issue 2004
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tagsanimals base sequence conserved sequence dna footprinting dna sequence analysis genes genomics humans mice nucleic acid sequence homology phylogeny rna splicing sequence alignment

ALGGENTool Content

http://alggen.lsi.upc.es/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

links directory index: 276
TitlePublication YearGoogle Scholar Citation Count
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters200640
FibreHelix, a program for calculating the X-ray diffraction pattern of macromolecules with helical symmetry: application to DNA coiled coils20052
MREPATT: detection and analysis of exact consecutive repeats in genomic sequences20036
Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN2003107
PROMO: detection of known transcription regulatory elements using species-tailored searches2002121
NAR Web Server Issue 2003
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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

AmoebaDB and MicrosporidiaDBDatabase Content

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

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Model Organisms > Databases

AmoebaDB and MicrosporidiaDB are functional genomic databases serving the amoebozoa and microsporidia research communities, respectively. AmoebaDB contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. MicrosporidiaDB contains the genomes of Encephalitozoon cuniculi, E. intestinalis and E. bieneusi. Genomic scale data can be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs, protein characteristics, phylogenetic relationships and functional data such as transcript (microarray and EST evidence) and protein expression data. Search strategies can be saved within a user's profile for future retrieval and may also be shared with other researchers using a unique strategy web address.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species20118
NAR Database Issue 2011
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tagsencephalitozoon entamoeba fungal genome genetic databases genomics protozoan genome

AnnotQTLTool Content

http://annotqtl.genouest.org [open in a new window]

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DNA > Annotations
DNA > Gene Prediction

AnnotQTL is a web tool for gathering functional and comparative information on a genomic region. It is designed to aggregate functional annotations from different websites by minimizing the redundancy of the information.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
AnnotQTL: a new tool to gather functional and comparative information on a genomic region20111
NAR Web Server Issue 2011
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tagsanimals cattle genomics humans livestock mice molecular sequence annotation quantitative trait loci

antiSMASHTool Content

http://antismash.secondarymetabolites.org [open in a new window]

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DNA > Annotations
Model Organisms > Microbes
Sequence Comparison > Multiple Sequence Alignments

The antibiotic and Secondary Metabolite Analysis Shell (antiSMASH) is a resource for identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

links directory index: 19
TitlePublication YearGoogle Scholar Citation Count
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences201119
NAR Web Server Issue 2011
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tagsbacteria bacterial genes bacterial genome biosynthetic pathways fungal genes fungal genome fungi genomics molecular sequence annotation peptide synthases polyketide synthases substrate specificity

ArchaeopteryxTool Content

http://phylosoft.org/archaeopteryx/ [open in a new window]

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DNA > Phylogeny Reconstruction

Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees.

links directory index: 51
TitlePublication YearGoogle Scholar Citation Count
phyloXML: XML for evolutionary biology and comparative genomics200951
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tagsbiological evolution computational biology genetic databases genomics phylogeny

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

ARGOTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/argo/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

ARGO is a tool for the detection and visualization of sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of eukaryotic genes.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters200514
NAR Web Server Issue 2005
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tagsalgorithms binding sites eukaryotic cells gene expression regulation genetic promoter regions genomics transcription factors

ArrayExpress updateDatabase Content

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

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Expression > Databases

The ArrayExpress Archive is a public repository of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus. The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy.

links directory index: 60
TitlePublication YearGoogle Scholar Citation Count
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments201160
NAR Database Issue 2011
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tagsgene expression gene expression profiling genetic databases genomics high-throughput nucleotide sequencing oligonucleotide array sequence analysis

ARTSDatabase Content

http://andromeda.gsf.de/arts [open in a new window]

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DNA > Sequence Polymorphisms
Model Organisms > Mouse and Rat

ARTS (Advanced Retrieval Tool for SNPs) can be used to retrieve SNP that are polymorphic between several different mouse strains to aid in the design of genome-wide SNP marker panels.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
ARTS: a web-based tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants200510
NAR Web Server Issue 2005
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tagsanimals chromosome mapping genetic markers genomics genotype inbred c3h mice mice mutant strains mice single nucleotide polymorphism

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

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

BAGELDatabase Content

http://bioinformatics.biol.rug.nl/websoftware/bagel/bagel_start.php [open in a new window]

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DNA > Gene Prediction
Model Organisms > Microbes

BActeriocin GEnome mining tooL (BAGEL) identifies putative bacteriocin ORFs (antimicrobial peptides) based on a database containing information about known bacteriocins and adjacent genes involved in bacteriocin activity.

links directory index: 48
TitlePublication YearGoogle Scholar Citation Count
BAGEL: a web-based bacteriocin genome mining tool200648
NAR Web Server Issue 2006
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tagsamino acid motifs bacterial genome bacteriocins genetic databases genomics multigene family open reading frames

BASysTool Content

http://basys.ca [open in a new window]

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DNA > Annotations
Model Organisms > Microbes

BASys (Bacterial Annotation System) is a tool for automated annotation of bacterial genomic (chromosomal and plasmid) sequences including gene/protein names, GO functions, COG functions, possible paralogues and orthologues, molecular weights, isoelectric points, operon structures, subcellular localization, signal peptides, transmembrane regions, secondary structures, 3-D structures, reactions, and pathways.

This content is being maintained by gary.vandomselaar@gmail.com.

links directory index: 78
TitlePublication YearGoogle Scholar Citation Count
BASys: a web server for automated bacterial genome annotation200578
NAR Web Server Issue 2005
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tagsbacterial chromosomes bacterial genome genomics plasmids

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