Finally, some of the pairwise alignments classified as young SDs may in fact not be young, but their high identity may have been maintained by gene conversion [ 6].
The soil types dominant along the proposed highway alignment were classified and characterized in strength.
On the lateral radiograph, stem alignment was classified as neutral, posterior or anterior.
The former alignment was classified as Main Road 93 and is now known as Delegate Road for most of its length.
If this probability is >0.5 (the closer to 1.0 this value is, the more confident is the prediction), the alignment is classified as "functional RNA", indicating that the sequence is from a potential RNA element in ncRNAs or a cis-regulatory element of mRNAs.
Therefore, positions of the alignment were classified into paired and unpaired states according to the consensus tRNA structure for the two sequences.
Query sequences with a significant hit (≥80% amino acid identity over ≥80% query length) to another alignment were classified as spurious and the corresponding twosome OG was removed from the analysis.
More specifically: All hits for a given read are sorted in decreasing as order as (1), as (2), … as (|M|) ; If both | as (2) - as (1) | > as t and | hs (2) - hs (1) | > hs t, where as t and hs t are predefined thresholds, the alignment is classified as unambiguous.
The total length of all uniquely aligned sequence was recorded and the resulting alignments were classified into three levels: Level 1: global alignment, do not allow gaps, strict threshold for score Level 2: global alignment, allow gaps, permissive threshold for score Level 3: local alignment, permissive threshold.
A bioinformatic pipeline and web tool were developed to describe the alignments of each library with the genome of the other species, and the alignments were classified into 5 different categories, according to the annotation associated with the sequence in each genome.
