lecture-7(宾夕法尼亚大学二代测序数据分析解析教程教本).pdfVIP

2013%%BMMB%597D:%Analyzing%Next%Generaon%Sequencing%Data% % %Week%4,%Lecture%7% IstvánAlbert Bioinformacs%Consulng%Center% % Penn%State% Connuing%lecture%6% •  The%BLAST+%binaries%have%been%downloaded% and%linked%into%the%bin%directory% % •  The%sequence%has%been%extracted%from%the% GFF%file% •  We%know%how%to%create%a%blast%database% makeblastdb%1parse_seqidsopon% •  Use%the%–parse_seqids%flag%when%invoking% makeblastdb% !%allows%the%retrieval%of%sequences% based%upon%sequenceiden9fiers.%% % •  In%that%case,%each%sequence%must%have%a%unique iden9fier,%and%that%idenfier%must%have%a%specific% format%% % see%also%secon%5.14%Limi)ng%a%Search%with%a%List% of%Iden)fiers!%in%the%BLAST+%handbook% ! •  This%is%an%advanced%opon%may%be%also%used%to%restrict%the%search%to%a% subset%of%sequences% More%files%are%created%!% FASTA%sequence%ID%format%values% blastdbcmd% •  A%useful%tool%with%an%unfortunate%name% •  and%unfortunate%parameters% •  and%unfortunate%documentaon% One%of%the%most%common%quesons% How%to%extract%a%% small%subsequence%from%a%genome?% There%are%a%number%of%answers%–%blastdbcmd%may%not%the%simplest%but%is%a%good%start% and%usually%you%already%have%the%commands%installed.% Displaying%the%content%of%% a%blast%database% See%the%help%% for%all%output%forma_ng%opons% Extract%regions%of%your%sequences% ~/bin/blastdbcmd-.db-refs/sc-.entry-all-.range-1.10- Fetch%a%subsequence%by%accesion% ~/bin/blastdbcmd-.db-refs/sc-.entry-chrV -.range-1000.1020- Batch%entries% Beware%of%tacit%behavior% Low%complexity%filter%is%ON%by%default% More%blast%query%out