We defined tandem duplication as one falling within 10 neighbors of another on genomic regions.
In this study, we defined tandem duplicated genes as adjacent homologous genes on a single chromosome, with no more than one intervening gene.
We defined tandem gene arrays as groups of genes that are located contiguously in a chromosome and that share a homology relationship.
For the identification of tandem duplicates, we first classified gene family using the software MCL with E value < 1E-10, and then defined tandem duplicates as follows: 1) belonging to the same gene family, 2) being located within 5 kb each other, and 3) being separated by ≤ 3 non-homologous genes.
One of the difficulties involved in locating tandem repeats is in accurately defining a tandem repeat.
Microsatellites have been defined as tandem direct repeats of motifs (subsequences) of one to six bases [ 1], and minisatellites as tandem direct repeats of longer motifs.
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In this study, scattered integration of the xylose assimilation genes PsXR, PsXDH and ScXK was investigated in Saccharomyces cerevisiae, and transcription analysis of these genes as well as their enzyme activities were compared with those observed when the genes were integrated into one single site (defined as "tandem integration" here).
Regarding this last mechanism, SSRs are defined as tandem repetitions of short motives and are largely accounted for as a source of genetic variability [2], [3] through the generally accepted slipped-strand mispairing mechanism [2], [4].
Microsatellite markers or simple sequence repeats (SSRs) are defined as tandem DNA repeats which are dispersed in both coding and non-coding regions along eukaryotic genomes.
