The resulting anchors consist of oriented genomic segments in two or more genomes that can contain mismatches, but no gaps, as provided by the alignment graph.
The structure of the human genome is highly variable and the copy number variations (CNVs) refer to alterations of genomic segments of more than 1,000 nucleotides that are present at significant frequencies within a population [ 17- 19].
Until recently, most of this genomic imbalance was diagnosed by cytogenetic analysis, but studies over the past few years have found that ID is caused by constitutional gains or losses of submicroscopic genomic segments even more often than by microscopically-apparent chromosomal aberrations [ 4- 6].
Therefore, at least 22 homeologous chromosomal pairs in rainbow trout, that contain two or more duplicated syntenic markers, can more reliably be assigned as the genomic segments that have originated following the salmonid specific duplication.
To control for a large number of genes being gained or lost by a large single genomic aberration event (i.e., whole chromosome loss), we also calculated the average number of SWITCHdna-defined segments and their length for each subtype, as more genomic breaks will result in more segments.
In particular, large genomic segments containing one or more genes can be duplicated or deleted, and segments can be 'horizontally transfered', i.e. taken from one organism's genome and inserted into another organism's genome.
These rearrangements are difficult to visualize without the help of rearrangement algorithms, sometimes involve local nested inversions (Fig. 6 ), but more generally encompass a gradual rearrangement of genomic segments of different lengths within and between chromosomes.
The 'raw' genome database included 301 935 distinct genomic segments (plasmids, chromosomes and other genomic segments) and contains 67 073 viral, 4366 bacterial and 236 archaea segments.
Genomic segments containing runs of five or more Ns were removed, as were transcripts with a MAKER-derived AED score > 0.2 (indicative of transcripts with lesser evidential support).
Bright red and green regions are genomic segments respectively amplified or deleted in more than 50% of the cells in the tumor samples.
