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Links tagged with 'cattle'

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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

Bovine Genome DatabaseDatabase Content

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

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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.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
Bovine Genome Database: integrated tools for genome annotation and discovery20116
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

LAGANTool Content

http://lagan.stanford.edu/lagan_web/index.shtml [open in a new window]

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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).

links directory index: 749
TitlePublication YearGoogle Scholar Citation Count
LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA2003749
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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

MAVIDTool Content

http://bio.math.berkeley.edu/mavid/download/ [open in a new window]

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DNA > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

MAVID performs multiple sequence alignments for large sequences, constructs phylogenetic trees and displays VISTA plots of conserved regions.

links directory index: 329
TitlePublication YearGoogle Scholar Citation Count
MAVID: constrained ancestral alignment of multiple sequences2004260
MAVID multiple alignment server200369
NAR Web Server Issue 2003
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tagsanimals base sequence cats cattle computational biology conserved sequence cystic fibrosis transmembrane conductance regulator dna sequence analysis dogs fishes genome genomics hiv-1 human genome humans mice molecular evolution molecular sequence data phylogeny rabbits rats sequence alignment simian immunodeficiency virus swine takifugu viral genome

ProbeLynxTool Content

http://www.pathogenomics.ca/probelynx [open in a new window]

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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.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
ProbeLynx: a tool for updating the association of microarray probes to genes200416
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/ [open in a new window]

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Protein > Proteomics

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

links directory index: 959
TitlePublication YearGoogle Scholar Citation Count
Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching1999959
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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/ [open in a new window]

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Protein > Domains and Motifs

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

links directory index: 21
TitlePublication YearGoogle Scholar Citation Count
QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns200521
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 [open in a new window]

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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.

links directory index: 22
TitlePublication YearGoogle Scholar Citation Count
Unique peptide identification of RNase A superfamily sequences based on reinforced merging algorithms20063
REMUS: a tool for identification of unique peptide segments as epitopes200611
A reinforced merging methodology for mapping unique peptide motifs in members of protein families20068
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

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