The simplest and fastest way to define loci within a chromosome alignment is to consider fixed-length intervals.
Threshold is the minimum number of read alignments required to consider there to be expression.
This is again why it's important that we choose the alignment to be considered over many projected cross-sections.
A minimum of 5 nt overlap per flanking junction sequence was required for alignment to be considered, selected on basis of maximizing overall alignment sensitivity (data not shown).
Perhaps more significantly, Berman et al. (2004) proposed the existence of 'preserved' binding sites, close enough in one genome to the analogous position in a sister genome to substitute functionally, but not close enough in a DNA sequence alignment to be considered conserved.
In deciding upon an aligner it is important to consider the alignment quality, ability to align large datasets, speed, dependence on a specific database, cost, and openness of the algorithm.
In this study, we use this idea to compare the most widely-used methods for pairwise structural alignment, in addition to considering alignment accuracy relative to other annotation sources: DSSP structural classes (Kabsch and Sander, 1983) and solvent accessibilities.
A suggested way to solve this problem is to consider alignment as a random variable, a strategy developed into the statistical alignment procedure [ 49, 50].
LocARNA achieves its short run-times for pairwise alignment because it needs to consider only significant base pairs.
First, it may be interesting to consider alignment of weighted PPI networks with weights representing, for instance, experimental evidence of interaction existence.
