RNA-Seq是新近開發出來的方法，用來分析包括基因和小分子RNA的轉錄。RNA-seq 是革命性的工具，改變轉錄體研究的程度和複雜性。研究人員利用RNA-seq的技術，可以有效地測量轉錄體數據的實驗，他們可以得到 如基因融合，差異表達基因，等位基因或小分子RNA，和轉錄後的基因突變存在。要利用這個強大的工具，我們需要新的方法和工具，以克服面臨的挑戰。在這篇論文中，我們提出這整合生物的知識和算法技術的系統，以提高轉錄分析的準確性和效率的方法。

The RNA-Seq is a recently developed method to profile transcriptome including mRNAs and small RNAs. This revolutionary tool for transcriptomics, RNA-seq, altered the view of the extent and complexity of transcriptomes. Using RNA-seq, researchers can efficiently measure transcriptome data experimentally, they can get information such as gene fusions, differential expression of alleles of genes, or existences of small RNA and post-transcriptional mutations. To harness this powerful tool we need new methods and tools to overcome the chanllenge which come with RNA-seq. In this thesis, we proposed methods and systems which integrate biological knowledge and algorithmic techniques to improve the accuracy and efficiency of transcriptome profiling.

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