TY - GEN
T1 - Reconfigurable hardware-software codesign methodology for protein identification
AU - Gudur, Venkateshwarlu Y.
AU - Thallada, Sandeep
AU - Deevi, Abhinay R.
AU - Gande, Venkata Krishna
AU - Acharyya, Amit
AU - Bhandari, Vasundhra
AU - Sharma, Paresh
AU - Khursheed, Saqib
AU - Naik, Ganesh R.
PY - 2016/10/18
Y1 - 2016/10/18
N2 - In this paper we propose an on-the-fly reconfigurable hardware-software codesign based reconfigurable solution for real-time protein identification. Reconfigurable string matching is performed in the disciplines of protein identification and biomarkers discovery. With the generation of plethora of sequenced data and number of biomarkers for several diseases, it is becoming necessary to have an accelerated processing and on-the-fly reconfigurable system design methodology to bring flexibility to its usage in the medical science community without the need of changing the entire hardware every time with the advent of new biomarker or protein. The proteome database of human at UniProtKB (Proteome ID up000005640) comprising of 42132 canonical and isoform proteins with variable database-size are used for testing the proposed design and the performance of the proposed system has been found to compare favorably with the state-of-the-art approaches with the additional advantage of real-time reconfigurability.
AB - In this paper we propose an on-the-fly reconfigurable hardware-software codesign based reconfigurable solution for real-time protein identification. Reconfigurable string matching is performed in the disciplines of protein identification and biomarkers discovery. With the generation of plethora of sequenced data and number of biomarkers for several diseases, it is becoming necessary to have an accelerated processing and on-the-fly reconfigurable system design methodology to bring flexibility to its usage in the medical science community without the need of changing the entire hardware every time with the advent of new biomarker or protein. The proteome database of human at UniProtKB (Proteome ID up000005640) comprising of 42132 canonical and isoform proteins with variable database-size are used for testing the proposed design and the performance of the proposed system has been found to compare favorably with the state-of-the-art approaches with the additional advantage of real-time reconfigurability.
KW - Finite state machines
KW - Hardware-software codesign
KW - Protein identification
KW - Reconfigurable systems
KW - String matching
UR - http://www.scopus.com/inward/record.url?scp=85009115419&partnerID=8YFLogxK
U2 - 10.1109/EMBC.2016.7591227
DO - 10.1109/EMBC.2016.7591227
M3 - Conference contribution
C2 - 28268821
AN - SCOPUS:85009115419
SN - 9781457702198
T3 - Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS
SP - 2456
EP - 2459
BT - 2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
PB - Institute of Electrical and Electronics Engineers Inc.
CY - Florida
T2 - 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2016
Y2 - 16 August 2016 through 20 August 2016
ER -
