lecture-21(宾夕法尼亚大学二代测序数据分析教程).pdf

2013%%BMMB%597D:%Analyzing%Next%Generaon%Sequencing%Data% % %Week%11,%Lecture%21% IstvánAlbert Biochemistry%and%Molecular%Biology%% and%Bioinformacs%Consulng%Center% % Penn%State% Genome%representaon%concepts% •  At%the%simplest%level%of%abstracon%the%genome%is%represented%by%a% one%dimensional%“space”%(lines)% % •  Genome%is%two%stranded%!%a%line%corresponds%to%each%strand% % •  Each%strand%has%a%polarity%!%each%line%has%a%direcon% % •  Strands%(lines)%are%paired%% % •  The%smallest%unit%is%one%base%!%one%integer%on%the%number%line% % •  Annotaons%(features)%are%segments%(coordinates)%on%each%line% Genomic%coordinates%–%brief%overview% DNA%two%stranded%and%direconal%% But%there%is%only%one%coordinate%system% % upstream%for%the%% forward%strand% 5’% 3’% 3’% 5’% upstream%for%the%% reverse%strand% 200% 300% Standard%formats%use%startend%even%for%the%reverse%strand% % The%upstreamregion–%before%the%5’%end%relave%to%the%direcon%of%transcripon% Coordinate%systems% •  0%based%!%0,%1,%2,%…%9% •  1%based%!%1,%2,%3,%…%10% % Typically% % •  0%based%are%noninclusiv