How to find/build the closest specie sequence database 如何在序列資料庫中找到最接近的目標物種

Take "Vibrio parahaemolyticus" for exmaple.
以腸炎弧菌(Vibrio parahaemolyticus)為例，

We cannot find this specie on common sequence database, ex: NCBInr.

一般在序列資料庫(如NCBInr)沒有細分到這一層，

If we cannot reduce possible sequence database pool, we'll get too much results too difficult to analysis.

如果不分類就搜尋的話，可能導致花費大量的時間在搜尋過程或結果的過濾上。

There are two ways to solve this issue.

因此可行的做法有2種，

One is to find the closest specie by lineage information,

一是找尋最接近的物種，

Another is to build the specific sequence database.

二是自行建立該特定物種的序列資料庫。

Two solutions are explained below:

以下分別說明:

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[Method 1] Find the closest specie by lineage information

[方法 1] 找尋最接近的物種

*. Input keyword "Vibrio parahaemolyticus" in http://www.uniprot.org/  then click "Search" button.

在 http://www.uniprot.org/ 中輸入 Vibrio parahaemolyticus 後按下 Search，

*. Click any protein  which its Organism belongs to "Vibrio parahaemolyticus", ex: Q87P32.

*. 再點擊任一個 Accession 其所屬的 Organism 是 Vibrio parahaemolyticus 之後 (如Q87P32)，

*. Click "Vibrio parahaemolyticus" link in Organism column.

選擇 Organism 的 Vibrio parahaemolyticus 連結，

*. Finally, you can find the lineage information in Lineage column.

*. 即可依循 Lineage 找出序列資料庫中最靠近的物種。

[Method 2] Build the specific sequence database.

[方法 2] 自行建立該特定物種的序列資料庫

*. On the last step in Method 1, click "UniProtKB" link.

方法 1中的最後一個步驟裡，選擊左上方的 UniProtKB 連結，

*. You will get the result that restrict to "Vibrio parahaemolyticus", then you can download sequence from this page.

*. 即可自動送出限定該物種的搜尋，以利該特定物種的序列資料庫的下載。

p.s. This skill also works on NCBI web.
Change Search value to "Protein" and input keyword "Vibrio parahaemolyticus".
After submit,  click link on Top Organisms area.

p.s. 類似步驟也可用在NCBI上，將 Seach 欄位改為 Protein，輸入關鍵字 "Vibrio parahaemolyticus" 後，即可在右方的物種點選連結，

You will get the result that restrict to "Vibrio parahaemolyticus".
If you need lineage information, click any protein.

點選後即會自動送出該物種的搜尋結果。

而如果需要 Lineage 資訊，再點選任一個protein，

Then click "Vibrio parahaemolyticus" link in ORGANISM column.

再點選 ORGANISM 中的 Vibrio parahaemolyticus 連結，

Click "Vibrio parahaemolyticus" link.

再點下 Vibrio parahaemolyticus 連結，

Finally, you will get the lineage information.

即可看到物種層次的關聯。