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本頁翻譯進度

燈號說明

審定:章彤輝(簡介並寄信)
翻譯:游佩芬(簡介並寄信)
編輯:朱學(簡介並寄信)

文獻搜尋

當想由原始文獻找出論文時,你會發現國家生物技術訓中心(National Center for Biotechnology Information- NCBI) 的網站相當好用。這個網站有個線上文獻搜尋的資源-PubMed 。許多標題與摘要可於PubMed 找到並可連結至相關論文的線上版本(PDF檔或全文) 。

另一個線上文獻搜尋的工具是科學資料庫網(Web of Science database) 。 這個工具在某些方面與PubMed相似,除了它並非強調醫學相關期刊,且包含沒被PubMed編入索引的期刊。

科學資料庫網亦能查詢科學引用指數(查詢某篇文章被引用之次數),這讓你可以得知哪些最近完成的論文曾引用你目前已蒐集的文獻。這種方式的搜尋對於跟上一個研究領域的最新知識是非常有幫助的。


去氧核糖核酸(DNA)序列分析

序列查詢可使用位於NCBI網站上GenBank內的許多查詢工具。其中以Entrez網頁最有價值,它可依據關鍵字找出DNA序列。

如果你有一段DNA序列並想得知是否與其他已知的DNA序列含有相同的序列片段,你可使用BLASTn這個工具。將你的序列輸入工具的視窗中,NCBI的伺服器將會把它與所有以知序列比對,抓出任何符合的資料。

另一方面如果你想知道兩個序列中是否有特別的相似區域,你可使用BLAST 2 序列工具(BLAST 2 Sequences tool) 。

在某些狀況下,你並不想查詢與你的序列相似的DNA序列,而可能會想找出有那些蛋白質與你的DNA序列可轉譯出的蛋白質序列相似。此時,可使用BLASTx工具。這個工具將你輸入的DNA序列轉譯成蛋白質並與已知的蛋白質序列或已知DNA序列所轉譯的產物比對。

當你想了解在細胞中不同的生化路徑是如何整合在一起,或者是你只想知道一個完整的生化代謝路徑的一部份,找一個有用的網站並放棄平時所熟讀的Stryer課本可能比較容易。京都基因與基因組百科(The Kyoto Encyclopedia of Genes and Genomes) 在提供這種部分代謝途徑的資料上非常好用。這個網站還提供與酵素,結構及其他有用的資料之連結。

如果你對分解外來毒物(環境毒素例如奈, 甲苯, 苯, 多氯化聯苯基等)的代謝途徑有興趣,可查詢The University of Minnesota Biocatalysis/Biodegradation Database的網站。


Literature Searches

When trying to identify papers from the primary literature, you may find it useful to use the National Center for Biotechnology Information (NCBI) website. This site hosts PubMed, an online literature search resource. Many of the titles and abstracts that can be reached through PubMed also have links to online versions (PDFs or full text versions) of the associated papers.

Another online literature search tool is the Web of Science database. This tool is similar in some respects to PubMed, except that it is not so strongly focused on medically-related journals, and includes journals not indexed on PubMed.

Web of Science also enables searches of the Science Citation Index, which allows you to ask the question, "What papers have been written recently that cite a paper I already have?" This type of search is very useful for keeping up-to-date in a research field.


DNA Sequence Analysis

Sequence searches can be carried out using the GenBank search tools available on the NCBI site. Most valuable of these is probably the Entrez browser, which can be used to find DNA sequences based upon keyword searches.

If you have a DNA sequence and would like to ask whether other sequences are known with homology to your sequence, use the BLAST tool (BLASTn). With this tool, you can paste your sequence into a window and the NCBI server will compare it to all known sequences, pulling up anything that matches.

On the other hand, if you have 2 sequences and want to know whether these two specifically match, you can use the "BLAST 2 Sequences tool".

In some cases, rather than searching for DNA sequences that closely match your own sequence, you may want to identify proteins whose sequences are homologous to those encoded by your DNA element. To do this, use the BLASTx tool. This tool will translate the DNA sequence you enter and will compare it to known protein sequences or translation products of known DNA sequences.

While trying to understand how different biochemical pathways fit together in a cell, or when you are simply trying to see a snapshot of an entire physiological pathway, it is often easier to forgo the usual perusal of Stryer and to instead find a useful website. The Kyoto Encyclopedia of Genes and Genomes is very useful for giving you such a snapshot of metabolism. The site also provides links to enzymes, structures and other useful information.

If you are specifically interested in pathways involved in the degradation of xenobiotics (nasty environmental toxins like naphthalene, toluene, benzene, PCBs, etc.) you may want to check out The University of Minnesota Biocatalysis/Biodegradation Database.


 
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