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Links tagged with 'cattle'

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AnnotQTLTool Content

http://annotqtl.genouest.org

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.

NAR Web Server Issue 2011
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tagsanimals cattle genomics humans livestock mice molecular sequence annotation quantitative trait loci

Bovine Genome DatabaseDatabase Content

http://BovineGenome.org

Model Organisms > Databases

The Bovine Genome Database (BGD) includes mechanisms too improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages. Genome browsers, available for both scaffold and chromosome coordinate systems, display the bovine Official Gene Set (OGS), RefSeq and Ensembl gene models, non-coding RNA, repeats, pseudogenes, single-nucleotide polymorphism, markers, QTL and alignments to complementary DNAs, ESTs and protein homologs. Researchers may upload their annotations to the BGD server for review and integration into the subsequent release of the OGS.

NAR Database Issue 2011
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tagsanimals cattle genetic databases genetic models genome genomics molecular sequence annotation quantitative trait loci sequence alignment systems integration

Ensembl Genome BrowserTool Content

http://www.ensembl.org/

DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Model Organisms > Other Organisms

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

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tagsanimals bacterial genome base sequence cattle computational biology database management systems dna sequence analysis dogs fungal genome gene expression genetic databases genetic polymorphism genetic variation genome genomics human genome humans invertebrates mice nucleic acid databases nucleic acid regulatory sequences plant genome protein databases proteins rats reference standards rna sequence alignment species specificity synteny systems integration tertiary protein structure transcriptional regulatory elements

GeneCodisTool Content

http://genecodis.dacya.ucm.es

Computer Related > Web Services
DNA > Annotations
Expression > Gene Set Analysis
Expression > Networks

Originally designed in 2007 for modular enrichment analysis, GeneCodis assists in functional analysis of gene lists, integrating information from different sources. GeneCodis also finds regulatory patterns, and singular and modular patterns of interrelated annotations.

NAR Web Server Issue 2009
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tagsanimals cattle gene expression regulation genes humans mice micrornas rats systems integration transcription factors

LAGANTool Content

http://lagan.stanford.edu/lagan_web/index.shtml

Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

The LAGAN alignment toolkit consists of components: CHAOS (a pairwise local aligner optimized for non-coding, and other poorly conserved regions of the genome.), LAGAN (a highly parametrizable pairwise global alignment program), Multi-LAGAN , and Shuffle-LAGAN (both variations of LAGAN).

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tagsanimals base sequence cattle chickens dna sequence analysis dogs genome human genome humans mice molecular sequence data nucleic acid sequence homology pan troglodytes papio rats sequence alignment swine takifugu zebrafish

ProbeLynxTool Content

http://www.pathogenomics.ca/probelynx

DNA > Tools For the Bench
Expression > Transcript Expression Analysis

Using current releases of genomic sequence data, ProbeLynx allows users to assess the specificity of probe sequences used for microarray experiments. The user provides probe sequences in FASTA or tab-delimited format, and ProbeLynx reports specificity information for each probe and functional annotations from Ensembl or TIGR for each probe target hit.

NAR Web Server Issue 2004
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tagsanimals base sequence cattle chickens complementary dna dna probes gene expression profiling genomics humans messenger rna mice nucleic acid databases oligonucleotide array sequence analysis oligonucleotide probes

ProteinProspectorTool Content

http://prospector.ucsf.edu/

Protein > Proteomics

Various tools used for sequence database mining in connection with mass spectrometry experiments.

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tagsanimals apolipoprotein a-i cattle factual databases mass spectrometry molecular weight protein disulfide-isomerases

QuasiMotiFinderTool Content

http://quasimotifinder.tau.ac.il/

Protein > Domains and Motifs

QuasiMotiFinder uses physicochemical similarity to PROSITE motifs and evolutionary conservation to predict sequence locations with possible function (pseudo-motifs).

NAR Web Server Issue 2005
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tagsamino acid motifs animals cattle conserved sequence furin logistic models molecular evolution protein sequence analysis sequence alignment

ReMusTool Content

http://140.121.196.30/remus.asp

Protein > 3-D Structure Retrieval/Viewing
Protein > Sequence Features

REinforced Merging techniques for Unique peptide Segments (ReMus) is designed for identification of the locations and compositions of unique peptide segments from a set of protein family sequences.

NAR Web Server Issue 2006
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals antibody specificity cattle chemical models computational biology conserved sequence epitope mapping epitopes humans mice molecular models molecular sequence data monoclonal antibodies pancreatic ribonuclease peptides protein conformation protein sequence analysis proteins sequence alignment structure-activity relationship

ScansiteTool Content

http://scansite.mit.edu/

Protein > Domains and Motifs

Scansite searches for motifs within proteins that are likely to be phosphorylated or that bind to common cellular signaling domains.

NAR Web Server Issue 2003
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tagsalgorithms amino acid motifs amino acid sequence animals binding sites cattle cdc2 protein kinase cdc2-cdc28 kinases computational biology consensus sequence cyclic amp-dependent protein kinases cyclin-dependent kinase 2 cyclin-dependent kinases factual databases fungal proteins genome humans mice mitogen-activated protein kinase kinases molecular models molecular sequence data molecular structure peptides phosphorylation protein binding protein conformation protein databases protein interaction mapping protein kinases protein sequence analysis protein-serine-threonine kinases proteins proteome rats saccharomyces cerevisiae proteins serine signal transduction substrate specificity tertiary protein structure threonine tyrosine

VISTATool Content

http://genome.lbl.gov/vista/index.shtml

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.

NAR Web Server Issue 2004NAR Web Server Issue 2007
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tagsalgorithms animals base sequence binding sites cats cattle chickens chromosome mapping computational biology dna dna sequence analysis dogs exons gene expression profiling genome genomics human chromosomes human genome humans kinesin leukemia mice molecular evolution molecular sequence data nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology pan troglodytes papio phylogeny rabbits rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism swine takifugu time factors transcription factors untranslated regions zebrafish