2007-01-012024-05-14https://scholars.lib.ntu.edu.tw/handle/123456789/655316摘要：本計畫負責cDNA序列、SNP分析及其功能註解之研發與應用，以往已進行超過10萬條序列之序列分析，其中包含了母豬早期胚、土雞產蛋相關、鵝隻肝臟及豬隻脂肪細胞等組織。當國外公開網站資料持續增加與修改，序列分析仍需要定期進行，並將這些分析結果依照條件建於本地端序列與註解資料庫，作為整體團隊的各樣分析之基礎。與子計畫3依照現行分析的流程建立分析系統，提供網路上自動化進行分析，讓未來的類似研究能夠快速獲取所需的分析結果，並將結果自動轉入資料庫中，使研究人員能夠繼續搜尋與擷取序列與註解資料。DNA序列身分註解之後，整合基因功能分類資料庫，依照母豬與土雞基因體蛋白質體研究團隊之需求，提供從序列比對到基因功能結合之資料庫系統，已經提供多個cDNA libraries的功能分析結果與相關實驗室，今年度預計將這些方法整理成系統(已有雞隻的基因功能分類系統雛型一套)，讓各基因體與蛋白質體實驗是能夠自行上網分析與查詢結果。晶片實驗室經常需要探針身分之查詢與整理，本計畫已經提供兩個晶片實驗室相關的探針資料，據以產生可查詢與整合之系統，讓晶片實驗室能夠依據其試驗所需查詢各種設計的基礎資料，今年度起將此查詢與整理方式轉成 網路介面的查詢整合系統，讓各晶片實驗室能夠依據其cDNA library與NCBI UniGene資料庫共同整理出合適的探針身分與試驗設計。針對cDNA序列上的SNP預測，使用各cDNA libraries註解資料，結合網路上公開之EST資料進行比對分析，已經發現多處cSNP，預計今年度建立整體查詢與分析系統。定期將國外網站之公開資料庫予以下載，並由子計畫3協助進行多方連結，配合本地端cDNA序列與註解資料庫，讓使用者透過網際網路得以快速搜尋與比較各項結果。另外提供子計畫1基礎資料，協助進行ORF, full-length, protein function預測，這些所需之 計算平台多由子計畫3提供。最終我們需要將這些完成的分析程式與條件都納入資料庫中提供web-based介面<br> Abstract: This project belongs to the bioinformatics development and application of functional genomics and proteomics to improve reproductive performance of breeding pigs and Taiwan country chicken project as the second subproject. This group is in charge of cDNA sequence/SNP analyses with their functions. There were more than 100,000 sequences (from more than 12 cDNA libraries) analyzed, which included sow early embryo, native country chicken of egg production, goose liver and porcine adipose tissue. Where the databases downloaded from the public domain increased and modified, the sequences of interest still need to rerun the sequence analysis. All the results will be saved into the new database with several ways. But, our techniques and research need to base on the results to verify. This subproject has cooperated with subproject 3 to implement a system of all the sequence analyses currently used for related researchers to search and retrieve those sequences and annotated information. We base on the needs from the team of sow/chicken genomics and proteomics studies to integrate gene function classification information from gene ontology and sequence annotation. We have provided the analyzed results to several labs. In addition, we also provided the basic information of probes for two microarray labs. This subproject is going to implement the analyses as two web-based systems. For SNP on cDNA sequences, we used cDNA annotation information for two libraries to compare with ESTs on the public databases. There have been a lot of cSNP found so far. The subproject will implement another system including cSNP analysis and public database of SNPs. We also provide the basic information of unique ESTs in each library for subproject 1 for executing prediction of ORF, full-length and protein function. For the above analyses, the subproject 3 assists us in the platform of computation.表現序列標誌生物資訊學單一核&#33527酸多型性繁殖性能Expressed Sequence TagBioinformaticsSingle Nucleotide PolymorphismReproductive Performance