Sentence examples for genomics browser from inspiring English sources
Upstream sequences (−1,000 to +200 relative to transcription start site or TSS) of the orthologous genes and their representative paralogs were extracted from reference genome sequences through the Gramene comparative genomics browser [ 35].
For the phenylpropanoid-lignin genes, the reported homologs of Arabidopsis47, poplar, rice29 and maize downloaded from the cell wall genomics browser (see URLs) were used as the seed sequences to detect the bamboo, Brachypodium and sorghum gene models by BLASTP with E values under 1 × 10−10 and with over 50% identity over the whole protein sequence.
Manual inspection of variant calls using a visualization tool such as the Integrative Genomics Browser (IGV) [ 21, 22] by a genomics expert is a potential alternative to our quality score threshold approach.
The outputs of the analysis, specifically the detected peaks were visualized in the Integrative Genomics Viewer genome browser [ 36].
In addition, the Micro-Tom SNPs are available from the Sol Genomics Network genome browser (http://solgenomics.net/gb2/gbrowse/ITAG2.4_genomic/).net/gb2/gbrowse/ITAG2.4_genomic/
To corroborate the informatics analysis, the peaks were manually visualized using the Integrative Genomics Viewer (IGV) genome browser [ 22].
Maps of the mouse compared to dog, rat, and human were retrieved from the Ensembl genome browser (Comparative Genomics - Synteny, http://www.ensembl.org/Mus_musculus/Location/Synteny) database.
To address this need, we developed Neisseria Base (NBase), a comparative genomics database and genome browser that houses and displays publicly available N. meningitidis genomes.
First, homologs of human host genes were found in vertebrate genomes using the Comparative Genomics panel of UCSC Genome Browser at http://genome.ucsc.edu[ 39].
The alignments of ESTs on the cucumber genome can be viewed on the cucumber genome browser in the Cucurbit Genomics Database [ 24].
In this study, we describe our construction of the Soybean Functional Genomics Database (SFGD) using Generic Genome Browser (Gbrowse) as the core platform.
