A total of 996 (34.2%) of the novel exons and 3,801 (23.8%) of the novel introns were also supported by EST alignments, which provides independent cDNA evidence for those events.
Further, 22,522 unigenes were annotated in the COG database via domain-based alignments, which provided a further 3,760 annotated unigenes.
Multiple sequence alignment can be easily performed using the "alignment" function, which provides two widely adopted multiple sequence alignment program MUSCLE [ 9] and ClustalW [ 10] with a number of advanced parameters.
Furthermore, we incorporate a spherical-harmonics-based fast subtomogram alignment algorithm, which provides a significant speedup.
Positive selection analysis was carried out on the full alignment length which provides the largest number of sites.
Hyaluronic acid was injected into a custom insertion tool (which provides alignment to the cochleostomy) for lubrication.
We identified individual missing exons or refined the boundaries of individual exons with the help of BLAT-based alignments and the 'Vertebrate Multiz Alignment & Conservation track' [ 59], which provides sequence-level genomic alignments for many vertebrate genomes.
Alignment was based on the identification of the mid-cycle 17β-estradiol drop (aligned cycle Day 0), which provides a reasonable estimate of the day of ovulation.
The flexible version of jFATCAT allows for the entry of twists in protein structures while matching their fragments, which provides better alignments in a number of cases.
