T cell receptor (TCR)可與抗原呈現細胞(MHC)共同辨認抗原並引起免疫反應。為了辨認大量的抗原，TCR會進行VDJ重組(VDJ recombination)來達到結構之多樣性。除了在免疫系統中有重要功能之外， VDJ重組對於疾病診斷和疫苗發展有很大關係。因此，將重組後的TCR序列比對至TCR基因上，以確定正確的VDJ組合，對於預防或治療疾病是很重要的。因為TCR基因上包含很多重複片段(Repeat)，一般的序列比對工具並不適用。因此，一些新的工具如SoDA與IMGT/HighV-Quest被提出，為針對重組後的TCR 序列的比對。測試許多資料後，我們仍然發現這些工具還是有不足的地方，因為他們序列比對的結果相似性(identity)都很低。這促使我們去開發一個更好的比對工具，稱為TCR-Aligner。TCR-Aligner整合了許多計算方法例如BLAST local alignment、global alignment及depth-first-search (DFS)，來提高比對重組後的TCR序列的準確性與靈敏度。在我們454定序TCRB的資料中，TCR-Aligner可以決定84.51%序列的VJ組合，高於SoDA (48.31%)和 IMGT/HighV-Quest ( 36.80%)，表示TCR-Aligner比對序列的靈敏度較高。更重要的為TCR-Aligner在序列比對的正確性最高。我們測試了四組定序資料中，TCR-Aligner的靈敏度與準確性均優於其他工具。由於VDJ重組對於免疫系統扮演很重要的角色，TCR-Aligner對於研究VDJ重組的領域應該會有很大的幫助。

T-cell receptor (TCR) can recognize antigen presented by major histocompatibility complex (MHC) and activate immune reactions. To recognize numerous antigens, T-cell receptor undergoes VDJ recombination for diverse structures. In addition to its vital roles in immune response, VDJ recombination has been implicated in disease diagnosis and vaccination. It is thus important to identify correct VDJ recombination for recombined TCR sequences by aligning them to the TCR genes. Because TCR genes contain a lot of repeats, common alignment tools are not suitable. As a result, new tools like SoDA and IMGT/HighV-Quest, have been recently proposed to align recombined TCR sequences. On several datasets, we found that some alignments by these tools were still not satisfying because the alignment identities were low. This motivated us to develop a better alignment tool, called TCR-Aligner. TCR-Aligner integrates several computational methods, e.g., BLAST local alignment, global alignment, and depth-first-search algorithm, to improve accuracy and sensitivity for aligning recombined TCR sequences. On our 454 TCRB datasets, TCR-Aligner aligned 84.51% recombined TCR sequences to the TCR gene higher than SoDA and IMGT/HighV-Quest (48.31% and 36.80%) did, respectively. More importantly, TCR-Aligner achieved higher alignment accuracy than other tools. The better performance of TCR-Aligner remained on three other datasets of distinct natures. Because VDJ recombination is essential in immune system, TCR-Aligner should directly benefit scientists in this field.

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