A Novel Signal Processing Measure to Identify Exact and Inexact Tandem Repeat Patterns in DNA Sequences

Abstract

The identification and analysis of repetitive patterns are active areas of biological and computational research. Tandem repeats in telomeres play a role in cancer and hypervariable trinucleotide tandem repeats are linked to over a dozen major neurodegenerative genetic disorders. In this paper, we present an algorithm to identify the exact and inexact repeat patterns in DNA sequences based on orthogonal exactly periodic subspace decomposition technique. Using the new measure our algorithm resolves the problems like whether the repeat pattern is of period or its multiple (i.e., 2, 3, etc.), and several other problems that were present in previous signal-processing-based algorithms. We present an efficient algorithm of , where is the length of DNA sequence and is the window length, for identifying repeats. The algorithm operates in two stages. In the first stage, each nucleotide is analyzed separately for periodicity, and in the second stage, the periodic information of each nucleotide is combined together to identify the tandem repeats. Datasets having exact and inexact repeats were taken up for the experimental purpose. The experimental result shows the effectiveness of the approach.

Identification of repeats in DNA sequences using nucleotide distribution uniformity

“…Table 1 shows that the perfect levels of periodicities 3 , 6 and 9 are similar, but the periodicity 3 has the largest mean NDU because of the highest copy number of periodicity 3. The periodicities in this DNA sequence identified by the proposed method are consistent with the EPSD method (Gupta et al, 2007). The results demonstrate the effectiveness of the proposed method in capturing different repeats and periodicities.…”

“…The effectiveness of the proposed algorithm is tested on Homo sapiens collagen type IV alpha 6 chain (COL4A6) (GenBankID:NC_001847, 6618 bp). This gene contains repeats of length 9 bp by the EPSD method (Gupta et al, 2007). The result by the DU method shows that the sequence contains repeats of 3 bp, 6 bp, 9 bp ( Fig.3(a)).…”

Searching microsatellites in DNA sequences: approaches used and tools developed

“…Therefore, a repeat sequence with smaller motif may go undetected or falsely detected (Gupta et al 2007;Zhou et al 2009). For example, a sequence (AT) 24 may be falsely detected as (ATATAT) 8 .…”

Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm

“…Available algorithms have some advantages and some disadvantages, as pointed out, for example in (36–39,42,72), and a systematic comparison of efficacy and applicability of different algorithms is still a challenge. It was pointed out that what is needed are systematic comparisons of efficacy and selectivity of different algorithms on the same, suitably selected standard set of test cases.…”