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Informative genes were re-annotated using the contig or EST from which the probe printed in the array was designed by comparing the referred sequence to the NCBI's nr database using the BLASTx algorithm as implemented by Blast2GO [ 67].
For each methylated (M) primer set, amplification of the fragment is dependent on methylation of the CpGs that are present in the sequence targeted by the "M" primer; while each unmethylated (U) primer set requires unmethylated CpGs in the referred sequence for amplification.
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The nomenclature of human KIAA0586 mutations refers to reference sequence NM_001244189.1 (corresponding protein: NP_001231118.1).
The resulting set of the unique sequences with associated read counts was referred as sequence tags.
All SNPs are referred using their reference sequence number (rs#).
In the HMM vector of Figure 1A, position numbers refer to the reference sequence of Nm.
GenBank accession numbers refer to reference sequences for each locus.
Then, duplicated sequences were removed from the initial dataset to produce a nonredundant set of unique sequences, hereafter referred to as sequence tags.
Duplicated sequences were eliminated from the initial dataset to produce a non-redundant set of unique sequences, hereafter referred to as sequence tags.
When a set of sequences (referred to as active sequences) are aligned, a distance between each pair of sequences can be calculated from the MSA.
The non-recombined sequences were aligned with ExPASy Decrease Redundancy tool, to identify the identical sequences (referred to as "redundant" sequences).
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