Splicing " enhancers " are sites to which splicing activator proteins bind, increasing the probability that a nearby site will be used as a splice junction.
12.
De novo Splice aligners allow the detection of new Splice junctions without need to previous annotated information ( some of these tools present annotation as a suplementar option ).
13.
Software tools that use genome-guided alignment include Bowtie, TopHat ( which builds on BowTie results to align splice junctions ), Subread, STAR, and Kallisto.
14.
The constants and the design parameters are linked by several logical and biochemical constraints ( e . g ., encoded automata theoretic variables must not be recognized as splicing junctions ).
15.
Senapathy has also shown that splice signal sequences that enable the spliceosome to recognize the splicing junctions originated from the stop-codon ends of Open Reading Frames ( ORFs ) in random sequence.
16.
Studies in evolution of eukaryotic genes and genomes involve the origin of exons, introns and splice junctions, as all eukaryotic genes are split into many exons separated by introns, whereas prokaryotic genes are not.
17.
In the splicing process the 5'end of the U1 snRNA forms complementary base pairing with the 5'splice junction of the inton to be excised, thus defining the 5'donor site of an intron.
18.
Using his split gene theory and S & S algorithm, Senapathy's team has developed analytical platforms and several database resources dedicated to the analysis of split genes, splice junctions, and mutations in several genomes including human, animals and plants.
19.
During the second step of splicing in eukaryotic cells, the EJC is deposited approximately 20-24 nucleotides from the 5 end upstream of the splice junction ( where two exons are joined ), when the lariat has formed and the exons are ligated together.
20.
The quality of a genome guided assembly can be measured with both 1 ) de novo assembly metrics ( e . g ., N50 ) and 2 ) comparisons to known transcript, splice junction, genome, and protein sequences using precision, recall, or their combination ( e . g ., F1 score ).
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