Sentence examples for alignment we define from inspiring English sources
For a given alignment, we define the amount of conserved sequence information as the number of bases in the reference sequence multiplied by the corresponding selection coefficient, which can be computed form the observed sequence identity by solving equation 1 for s (see Methods for more details).
Using these alignments, we defined novel transcribed genomic regions as those with a read depth ≥10.
Where there was a gap (with the minimal length of 2 genes) in only one chromosome in the multiple alignments, we defined it as an indel.
From the 579 alignments, we defined three data sets with different genomic, evolutionary and phylogenetic meaning: - ' Blochmannia' core: composed by the 579 annotated protein coding genes of Blochmannia floridanus and their corresponding homologs in the other 20 genomes.
Using the Mauve alignment tool,, we defined 42 local collinear blocks (LCBs) with highly similar sequence stretches in human and chimpanzee.
We therefore recalculated all of the fungal substitution rates using only high quality regions of the pairwise alignments, which we defined to be a concatenation of blocks containing a minimum of 10 consecutive aligned amino acids with no gaps.
In the second section we define alignments formally and state a few main results on the statistics of local sequence alignment.
(We define the alignment of the cell as the alignment of the ellipse that best fits the cell shape).
Note that since we are considering RNA-to-DNA alignments from an RNA contig-centric perspective (i.e. we define an alignment as a single mapping for each position in a contig sequence), we are not concerned with deletions, i.e. unaligned genomic positions flanked by aligned genomic positions, which would typically represent introns in RNA-to-DNA alignments.
On the basis of these choices we define the alignment algorithm, which has been implemented in MP-Align.
We define any alignment with P value less than or equal to 0.05 as being "above noise".
