组装序列 - 系统生物学暨网路生物学实验室.ppt

* PURPOSE Providing more gene information of L. vannamei by integrate functional and comparative genomics. * EST of the white shrimp from NCBI Daphnia pulex as reference genome Annotated the ESTs of white shrimp Comparative analysis * * * MATERIALS AND METHODS * MATERIALS AND METHODS Litopenaeus vannamei Eukaryota Metazoa Arthropoda Crustacea Malacostraca Eumalacostraca Eucarida Decapoda Dendrobranchiata Penaeoidea Penaeiodae Litopenaeus * 資料來源:國立台灣海洋大學典藏甲殼類標本資料庫 * MATERIALS AND METHODS Daphnia pulex Eukaryota Metazoa Arthropoda Crustacea Branchiopoda Diplostraca Cladocera Anomopoda Daphniidae Daphnia * /Dappu1/Dappu1.home.html L.v est Water fleas genome (transcript) blast 挑選best hit hit到同一個gene的est 無法黏至任一個gene的est cluster together de novo assembly assembly contig contig no assembly * ANALYSIS PIPELINE * contig no assembly domain mapping similarity search comparative analysis physiology comparative Drosophila comparative other penaeid shrimps Gene Ontology UniProt KEGG ppi * * ANALYSIS PIPELINE * RESULTS * * RESULTS L. vannamei (ESTs) D. pulex (transcripts) sequence number 161241 30907 average length 494 1061 maximum length 2143 24144 minimum length 19 150 GC ratio 0.43 0.46 * * ANTICIPATED RESULT physiology comparative hepatopancreas gill hemocytes * ventral nerve cord eyestalk * P.monodon F.chinesis M.japonicus L.vannamei ANTICIPATED RESULT white shrimp v.s other penaeid shrimp * * ANTICIPATED RESULT White shrimp v.s Drosophila Drosophila L.vanna