Sentence examples for using the genomic coordinates from inspiring English sources

Using the genomic coordinates provided by the Rat Genome Database [ 20], the QTL intervals cover a total of ~860 Mb bp, or 33% of the entire rat genome.

Next, using the genomic coordinates of all Refseq genes, we look for duplicated regions that overlap genes.

The alignment between the transcript coding for the interacting protein and each isoform was done using the genomic coordinates of the coding sequences provided by Ensembl.

If the TSS of an organism are known, one may guide the gene annotation process by using the genomic coordinates of the TSS as constraints for gene prediction.

Individual segments of a gene region (i.e. the 10 kb sequence upstream of a TSS, the 5' and 3' UTRs and the CDS) for each mature gene encoding reference sequence (RefSeqs with NM prefixed identifiers) were determined using the genomic coordinates within the refGene databases (Additional File 3).

Since the exact boundaries of miRNA genes (including regulatory elements) are difficult to determine, we used the genomic coordinates of all pre-miRNA loci deposited in miRBase (v 13.0; N = 715) as a proxy of miRNA gene sequences (three pre-miRNA loci located in the mitochondrial genome were excluded from our analysis) [ 33, 34].

We used the genomic coordinates for exons 1 and 2 of the Nlrp1b CCDSSV1 (CCDS 36210) and C57-SV3 (CCDS 48839) reported at the NCBI Consensus Coding sequence (CCDS) database (http://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi) (assembly MGSCv37) to analyze the corresponding loci for exon 1 and 2 in the genome sequence of CAST/EiJ, available at Sanger (http://www.sanger.ac.uk).sanger.ac.uk

The second phase, C himeric Transcript Sequence Reconstruction and Domain Annotation, includes two steps: i) reconstruction of the chimeric transcript using the genomic breakpoint coordinates and the partner gene annotations ii) annotation of the assembled sequence to provide information on the fusion frame and to generate a report of all the protein domains conserved or lost in the gene fusion.

Given the sequences of the promoters on the ChIP array, a Perl script was used to automate BLAST searches of alignment across the genome and screen the BLAST output and BioPerl was used to extract the genomic coordinates of the promoters.

BEDTools (Version 2.9.0) (Quinlan and Hall, 2010) was used to compare the genomic coordinates to find reads overlapping with mature miRNAs.

LiftOver [ 31], a tool at UCSC for conversion of genome coordinates between assemblies either within a species or between species, was used to convert the genomic coordinates of all human CREs to mouse, rat and dog coordinates.