TY - GEN
T1 - Application of the Burrows-Wheeler transform for searching for approximate tandem repeats
AU - Danek, Agnieszka
AU - Pokrzywa, Rafał
AU - Makałowska, Izabela
AU - Polański, Andrzej
PY - 2012
Y1 - 2012
N2 - Tandem repeats (TRs) are contiguous copies of repeating patterns, which may be either exact or approximate. Approximate tandem repeats (ATRs) in a genomic sequences are adjacent copies of a repeating pattern of nucleotides, where similarity is defined by a suitable measure. Both TRs and ATRs are used in forensic analysis, DNA mapping, testing for inherited diseases and many evolutionary studies. All their functions and roles are not well defined and remains a subject of ongoing investigation. However, growing biological databases together with tools to look for such repeats may lead to better understanding of their behavior. This paper presents our method for searching for ATRs defined on the basis of the model of substitution mutations and its comparison to two other tools. The capabilities and limitations of methods are analyzed and results obtained with each tool are investigated.
AB - Tandem repeats (TRs) are contiguous copies of repeating patterns, which may be either exact or approximate. Approximate tandem repeats (ATRs) in a genomic sequences are adjacent copies of a repeating pattern of nucleotides, where similarity is defined by a suitable measure. Both TRs and ATRs are used in forensic analysis, DNA mapping, testing for inherited diseases and many evolutionary studies. All their functions and roles are not well defined and remains a subject of ongoing investigation. However, growing biological databases together with tools to look for such repeats may lead to better understanding of their behavior. This paper presents our method for searching for ATRs defined on the basis of the model of substitution mutations and its comparison to two other tools. The capabilities and limitations of methods are analyzed and results obtained with each tool are investigated.
KW - Burrows-Wheeler transform
KW - Hamming distance
KW - approximate tandem repeats
KW - suffix array
UR - https://www.scopus.com/pages/publications/84868700657
U2 - 10.1007/978-3-642-34123-6_23
DO - 10.1007/978-3-642-34123-6_23
M3 - Conference contribution
AN - SCOPUS:84868700657
SN - 9783642341229
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 255
EP - 266
BT - Pattern Recognition in Bioinformatics - 7th IAPR International Conference, PRIB 2012, Proceedings
T2 - 7th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2012
Y2 - 8 November 2012 through 10 November 2012
ER -