Minimum requirements for annotation were a contiguous alignment of 300 bp, with 85% sequence similarity and a minimum e-value of 1 × 10−20.
The segment (35%) at the top of group F had a dense contiguous alignment spanning the initial 28% of Mt-2.
We generated a presumptive locus assembly of ordered/oriented spretus contigs that maximizes contiguous alignment between the two species (Fig. 1).
To get the best possible contiguous alignment, each raspberry unigene was compared to its best CDS match in each of the three genomes with SSearch [ 68], a software program that performs a rigorous Smith-Waterman alignment.
It impresses for many reasons, not the least of which is that the artist brings the ghoulish and decorative into contiguous alignment.
We used these contiguous alignment regions as conserved regions, which occupy 44% (1,255,655,305/2,818,767,476 bases, excluding the Y chromosome and gaps between contigs) of the human genome, which is almost the same percent (roughly 40%) as that detected by the previous study [ 20] of the mouse genome using BlastZ.
This correction is needed to obtain the percentage of net alignment, thus hiding the effects of non-contiguous alignment regions.
Each of 473 files totaling 2.837 Gbp of DNA was identified by chromosome and order, allowing the alignment of contiguous DNA fragments from each chromosome.
Thus, for a subset of class A, we added to the MSA of the 7-TMs the alignment of 5 contiguous EL2 residues.
The random variable X represents the count of SNPs in contiguous 100 kb intervals from an alignment of two human genomes.
