title: Reconfigurable hardware-software codesign methodology for protein identification.
abstract: 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.
authors.forename: Venkateshwarlu Y
authors.initials: VY
authors.lastname: Gudur
authors.forename: Sandeep
authors.initials: S
authors.lastname: Thallada
authors.forename: Abhinay R
authors.initials: AR
authors.lastname: Deevi
authors.forename: Venkata Krishna
authors.initials: VK
authors.lastname: Gande
authors.forename: Amit
authors.initials: A
authors.lastname: Acharyya
authors.forename: Vasundhra
authors.initials: V
authors.lastname: Bhandari
authors.forename: Paresh
authors.initials: P
authors.lastname: Sharma
authors.forename: Saqib
authors.initials: S
authors.lastname: Khursheed
authors.forename: Ganesh R
authors.initials: GR
authors.lastname: Naik
mesh_terms: D003201:Computers; D030562:Databases, Protein; D006801:Humans; D011506:Proteins / Q000032:analysis*; D012984:Software; D013997:Time Factors
chemical_list: D011506:Proteins