SEQUENCE GRAPH-BASED TOOL FOR DETERMINING VARIATION IN SHORT TANDEM REPEAT AREAS Russian patent published in 2023 - IPC G16B20/00 

FIELD: bioinformatics.

SUBSTANCE: described embodiments relate to methods, devices, systems for genotyping repeat sequences, including short tandem repeats (STR), that are medically significant. The methods include aligning reads with a repeat sequence represented by a sequence graph and using the aligned reads to genotype the repeat sequence. A sequence graph is a directed graph that includes at least one simple cycle of its own, representing a subsequence of repetitions. In some embodiments, the reads are paired-end reads, and both conjugated reads of each pair of reads can be used to genotype repeat sequences. Some implementations can be used to determine the repeats of degenerate codons. Some implementation options can be used to genotyping repeat sequences, each of which includes two or more repeat subsequences. Some implementation options can be used to genotyping nucleotide sequences, each of which includes at least one repetitive subsequence and another genetic variant, such as an insertion, deletion or substitution.

EFFECT: invention expands the arsenal of means for genotyping.

31 cl, 7 dwg, 1 tbl, 1 ex