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Bit-parallelism score computation with multi integer weight
Setyorinia,b, Kuspriyantoa, Widyantoro D.H.a, Pancoro A.a
a School of Electrical Engineering and Informatics, Institut Teknologi Bandung, Indonesia
b School of Computing, Telkom University, Indonesia
[vc_row][vc_column][vc_row_inner][vc_column_inner][vc_separator css=”.vc_custom_1624529070653{padding-top: 30px !important;padding-bottom: 30px !important;}”][/vc_column_inner][/vc_row_inner][vc_row_inner layout=”boxed”][vc_column_inner width=”3/4″ css=”.vc_custom_1624695412187{border-right-width: 1px !important;border-right-color: #dddddd !important;border-right-style: solid !important;border-radius: 1px !important;}”][vc_empty_space][megatron_heading title=”Abstract” size=”size-sm” text_align=”text-left”][vc_column_text]© 2019, School of Electrical Engineering and Informatics. All rights reserved.Dynamic Programming (DP) is still the core algorithm in many biological analysis tools, especially similarity analysis. DP always promises optimal solutions, but as the size and number of sequences increase, time performance decreases. This makes various researches related to the improvement of time performance offered. Performance improvement is offered by adding process units that work together in parallel environments or reducing the accuracy by only calculating the input part. Bit-parallelism offers an increase in speed by changing the score matrix process unit to a larger process unit, namely word. Then this word unit will be processed in parallel like word processing on a computer system. Bit-parallelism has been successfully applied to cases with simple weights such as LCS and Edit Distance. Applications in more complex cases, namely with integer weights also exist, but still assume an integer weight for match representation. In the case of protein alignment where there is more than one integer value to represent the match of the residual pair, this solution cannot be applied directly. This paper presents a preliminary research on how to formulate a computational algorithm score bitparallelism with multi-integer weights. The solution offered is the development of General Integer scoring, by applying functional multi tables. The results show that the algorithm is able to obtain the same score matrix as the DP score matrix, with computing O(m), m is size of the sequence, and O(b) space where b is the range of integer set weights.[/vc_column_text][vc_empty_space][vc_separator css=”.vc_custom_1624528584150{padding-top: 25px !important;padding-bottom: 25px !important;}”][vc_empty_space][megatron_heading title=”Author keywords” size=”size-sm” text_align=”text-left”][vc_column_text][/vc_column_text][vc_empty_space][vc_separator css=”.vc_custom_1624528584150{padding-top: 25px !important;padding-bottom: 25px !important;}”][vc_empty_space][megatron_heading title=”Indexed keywords” size=”size-sm” text_align=”text-left”][vc_column_text]Bit-parallelism,Dynamic programming,General integer scoring,Sequence alignment[/vc_column_text][vc_empty_space][vc_separator css=”.vc_custom_1624528584150{padding-top: 25px !important;padding-bottom: 25px !important;}”][vc_empty_space][megatron_heading title=”Funding details” size=”size-sm” text_align=”text-left”][vc_column_text][/vc_column_text][vc_empty_space][vc_separator css=”.vc_custom_1624528584150{padding-top: 25px !important;padding-bottom: 25px !important;}”][vc_empty_space][megatron_heading title=”DOI” size=”size-sm” text_align=”text-left”][vc_column_text]https://doi.org/10.15676/ijeei.2019.11.1.3[/vc_column_text][/vc_column_inner][vc_column_inner width=”1/4″][vc_column_text]Widget Plumx[/vc_column_text][/vc_column_inner][/vc_row_inner][/vc_column][/vc_row][vc_row][vc_column][vc_separator css=”.vc_custom_1624528584150{padding-top: 25px !important;padding-bottom: 25px !important;}”][/vc_column][/vc_row]