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Four non-redundant full-length cDNAs were aligned to mouse genomic DNA (derived from the UCSC mouse genome) to infer exon-exon boundaries and to derive alternatively spliced exons (Fig. 1A).
Unlike in the Human Genome Project, teams will be able to request regions of the mouse genome to sequence first.
Using this approach, investigators have succeeded at introducing specific mutations in the mouse genome to study genes of previously unknown function, or to restore the function of inactive genes.
Using the BLAST algorithm, the obtained sequences were aligned to the mouse genome to identify the integration sites.
Luciferase oligos were blasted against the mouse genome to ensure that they do not recognise any sequence in the mouse DNA.
Birzele et al. [12] used transcripts from the closely related mouse genome to cluster short reads for assembly leading to a reduction in their contig set of approximately 6% to 92,272 contigs with a mean length of 352 bp.
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Here we administer a bioinformatics search strategy to the human and mouse genomes to explore the landscape of A-to-I RNA editing.
It is now relatively straightforward to apply tools developed for human and mouse genomes to a few well-assembled and annotated livestock genomes.
Based on an analysis of EST sequences, the zebrafish genome, similar to the mouse genome, appears to code only for the short isoform (Fig. S1A).
Each transcript was aligned to the Celera mouse genome sequenced to define the exon structure [ 30].
The region of the mouse genome corresponding to the MIR element, according to the UCSC genome-genome alignment, is the complement strand of hg18 chr13:9,634, 994-9, 635, 139.
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Justyna Jupowicz-Kozak
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