dc.contributor.author |
Prakasam, Elakkiya |
|
dc.contributor.author |
Manoharan, Arun |
|
dc.date.accessioned |
2022-10-30T21:25:38Z |
|
dc.date.available |
2022-10-30T21:25:38Z |
|
dc.date.issued |
2022-10-30 |
|
dc.identifier.issn |
2210-142X |
|
dc.identifier.uri |
https://journal.uob.edu.bh:443/handle/123456789/4667 |
|
dc.description.abstract |
K-mer (k length substrings in a DNA sequence) counting plays an important role in genome assembly, sequence analysis, and error correction in sequence reads. In the Gene data sets, a single occurrence of k-mers occupies more storing space with a higher possibility of sequencing errors. Hence, error correction plays a significant role in eradicating such uninformative k-mers. Bloom filters data structure has been frequently used in k-mer counting for determining thek-mer occurence at least twice in a data set of a DNA sequence owing to its less memory usage and its fast querying. The standard bloom filer used in k-mer counting is not cache efficient as it accesses the whole bloom filter memory for single k-mer insertion/query. Also the Murmur hash consumes more time for hashing the k-mers from the Input Sequence. In this proposed work, we have improved the process of k-mer counting further by adopting different bloom architecture called a partitioned bloom data structure. The proposed architecture is cache efficient and uses only one memory access instead of in the standard bloom filte’s k memory accesses. The rolling hash in ntHash function is used for hashing the k-mers from the input sequence has further reduced the hash computation time of k-mers. The proposed architecture was compared with standard architecture and the results showed that the proposed k-mer counter minimized significantly the k-mers loading and querying time from the memory for different data sets. |
en_US |
dc.language.iso |
en |
en_US |
dc.publisher |
University of Bahrain |
en_US |
dc.subject |
K-mer counting, Bloom filter,Recursive Hash function,Genome Assembly |
en_US |
dc.title |
Performance Improvement of K-mer counting in DNA Sequence using Cache efficient Bloom filter and recursive hash function |
en_US |
dc.type |
Article |
en_US |
dc.identifier.doi |
https://dx.doi.org/10.12785/ijcds/120182 |
|
dc.volume |
12 |
en_US |
dc.issue |
1 |
en_US |
dc.pagestart |
1019 |
en_US |
dc.pageend |
1027 |
en_US |
dc.contributor.authoraffiliation |
School of Electronics Engineering,Vellore Institute of Technology, Vellore, Tamilnadu, India |
en_US |
dc.source.title |
International Journal of Computing and Digital Systems |
en_US |
dc.abbreviatedsourcetitle |
IJCDS |
en_US |