Exact and Approximate Repeats in DNA Sequences using Suffix Array and Divide & Conquer

Author Name(s): *Raju Bhukya,Priyanka Agrawal, Rajmani Arya, Shekhar Prasad
Author Email: drrajunitw@gmail.com

Abstract

Microsatellites or Simple Sequence Repeats are short motifs, for the most part 2-8 base pairs long that are repeated numerous times in genomic DNA. Here, motifs are short, repeating patterns in DNA that have an organic capacity. These SSRs are responsible for sequence-binding locations for proteins like Transcription factor. Such groupings are extremely normal over the eukaryotic genomes and are found in plenitude with variable recurrence of event. In the event that the rates of transformations at the repeat loci is observed to be high contrasted with different locales of genomic DNA it can often lead to generation of inter and intra-specific hereditary variety, and thus permit their hereditary marker exploitation. Recent evidences demonstrate the auxiliary and utilitarian essentialness of microsatellites and have consequently made it an imperative subject in contemporary research in addition to their time–proven use as an efficient molecular marker system. Taking after the transformation in sequencing advances, even the extent that non model life forms are concerned, the whole genomes can now be possibly screened utilizing bio tools to locate the presence of SSRs.

Introduction

Repeats in DNA successions comprise of short arrangements or examples that repeat. These repeats can be either scattered or tandem. Blended repeats are long, less incessant and far separated while tandem rehashes are continuous events of an example that are contiguous each other. These repeats examples are either precise or there might be inclusion or deletion or substitution of a base, because of transformations, as needs be there are correct and surmised pair rehashes. Pair repeats are additionally grouped into microsatellites, mini-satellites and satellite DNA in light of the time of the repeat. Rehashes comprising of under 1 to 6 nucleotides are alluded to as microsatellites. Small scale satellites are those that have a period estimate more prominent than 6 nucleotides and satellite DNA have more noteworthy than 100 nucleotides. Tandem repeats are identified with numerous human illnesses brought about by hereditary issue, for example, Huntington’s infection, delicate X mental impediment, ‘myotonic dystrophy’, strong decay

Conclusion

Our program can find repeats of motif length in a given range with given maximum period limitation. We have modified the algorithm proposed by Main and Lorentz to find approximate tandem repeats by introducing a tolerance factor. Further this algorithm can be improved by applying Euclidean distance or edit distance because hamming distance has many drawbacks it only calculates character to character mismatch while edit distance can calculate score based on insertion, replacement or deletion by giving weight to each type of operation. The algorithm can also be useful in DNA compression (e.g. replacing ‘xxxx’ as ‘x4’ where ‘x’ is a repeating unit) and in DNA pattern recognition. For large DNA sequences greater than 100 MB can’t be processed on simple system so parallel programming concept can enhance the memory and time efficiency of this program. Parallel programming concept can be applied easily to divide and conquer method.

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