?url_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rft.relation=http%3A%2F%2Fmiis.maths.ox.ac.uk%2Fmiis%2F285%2F&rft.title=A+two-base+encoded+DNA+sequence+alignment+problem+in+computational+biology&rft.creator=Chang%2C+Jen-Mei&rft.creator=Drakes%2C+Chiaka&rft.creator=Huang%2C+Erya&rft.creator=Langat%2C+Deidrey&rft.creator=McGrath%2C+Joseph&rft.creator=Morabito%2C+Mark&rft.creator=Pacheco%2C+Jose&rft.creator=Rodriguez%2C+Nancy&rft.creator=Salazar%2C+Daniel&rft.creator=Vemuri%2C+Rao&rft.creator=Vu%2C+Man&rft.creator=Wadhar%2C+Hem&rft.creator=Wu%2C+Qin&rft.subject=Medical+and+pharmaceutical&rft.description=The+recent+introduction+of+instruments+capable+of+producing+millions+of+DNA+sequence+reads+in+a+single+run+is+rapidly+changing+the+landscape+of+genetics.+The+primary+objective+of+the+%22sequence+alignment%22+problem+is+to+search+for+a+new+algorithm+that+facilitates+the+use+of+two-base+encoded+data+for+large-scale+re-sequencing+projects.+This+algorithm+should+be+able+to+perform+local+sequence+alignment+as+well+as+error+detection+and+correction+in+a+reliable+and+systematic+manner%2C+enabling+the+direct+comparison+of+encoded+DNA+sequence+reads+to+a+candidate+reference+DNA+sequence.%0D%0A%0D%0AWe+will+first+briefly+review+two+well-known+sequence+alignment+approaches+and+provide+a+rudimentary+improvement+for+implementation+on+parallel+systems.+Then%2C+we+carefully+examin+a+unique+sequencing+technique+known+as+the+SOLiDTM+System+that+can+be+implemented%2C+and+follow+by+the+results+from+the+global+and+local+sequence+alignment.%0D%0A%0D%0AIn+this+report%2C+the+team+presents+an+explanation+of+the+algorithms+for+color+space+sequence+data+from+the+high-throughput+re-sequencing+technology+and+a+theoretical+parallel+approach+to+the+dynamic+programming+method+for+global+and+local+alignment.+The+combination+of+the+di-base+approach+and+dynamic+programming+provides+a+possible+viewpoint+for+large-scale+re-sequencing+projects.+We+anticipate+the+use+of+distributed+computing+to+be+the+next-generation+engine+for+large-scale+problems+like+such.&rft.date=2009&rft.type=Study+Group+Report&rft.type=NonPeerReviewed&rft.format=application%2Fpdf&rft.language=en&rft.identifier=http%3A%2F%2Fmiis.maths.ox.ac.uk%2Fmiis%2F285%2F1%2F4_National_Institute_of_Genomic_Medicine.pdf&rft.identifier=++Chang%2C+Jen-Mei+and+Drakes%2C+Chiaka+and+Huang%2C+Erya+and+Langat%2C+Deidrey+and+McGrath%2C+Joseph+and+Morabito%2C+Mark+and+Pacheco%2C+Jose+and+Rodriguez%2C+Nancy+and+Salazar%2C+Daniel+and+Vemuri%2C+Rao+and+Vu%2C+Man+and+Wadhar%2C+Hem+and+Wu%2C+Qin++(2009)+A+two-base+encoded+DNA+sequence+alignment+problem+in+computational+biology.++%5BStudy+Group+Report%5D+++++