u100023046's blog

尋找所需要的fasta序列，以curcuma longa為例

利用blastn的方式選取不同種的curcuma

在存檔的地方選有aligned的選項，載下來的檔案是txt檔，可利用更改副檔名的方式，將它存為fasta檔

再利用MEGA進行一次Alignment

進入後

在phylogeny的地方接選取Bootstrap method

即可得到

Q1: Install the melanie view (Viewer_v502.exe):

Analyze the gel on folder \gels\94-0002.mel, 94-0005.mel, and ECOLI.mel

1.Which is the most abundant protein in gel ECOLI.mel in the region range from pH 5.5-6, MW 16k-32k Da, please answer with the protein name, official name, accession number, %vol, measured pI/MW, theoretic pI/MW

2.Set ECOLI as reference gel, select as group on three gels, and analyze the expression ratio of above protein in the three gels. (ECOLI : 94-0005 : 94-0002)

–

Q2: A MS/MS data of spotX from bacteria was obtain in next slide with m/z lists.

–what this protein is (protein name, gene name, accession number)

1. dbSNP    gene

(1)在搜尋欄輸入BRCA1
(2)限制條件
(3)縮小至15件

2.SNP500Cancer     gene

3.HapMap      CHB    注釋 TAG SNP

選取紅色框框處

在紅色框框處輸入BRCA1，即可得到圖

1.BLASTn

2.Biology workbench-cluster w

從這張圖可以知道有兩種的核甘酸序列是接近的

3.ePCR-ucsc genome browser

利用這個軟體做不同物種的比對，但由於我的序列是取至植物

與人體比對並無重疊

1. Write down a chemical name

Atrazine
2. Find out experiment data in the database

http://lmmd.ecust.edu.cn:8000/search/?cas_rn=&common_name=Atrazine&iupac_name=&smiles=&action=A

3. Predict ADMET of the chemical

http://lmmd.ecust.edu.cn:8000/predict/?smiles=CCNc1nc%28NC%28C%29C%29nc%28n1%29Cl&action=A

4. Discuss the potential effects induced by a chemical

此化合物不算致癌物，但是它具有致癌的毒性，而且具有高的Tetrahymena Pyriformis Toxicity，除此之外他也不具有AMES毒性。

1) Write down the names of your interested chemical.

Atrazine

http://ctdbase.org/detail.go?type=chem&acc=D001280

2) Use CTD to identify
–a) Diseases

http://ctdbase.org/detail.go?type=chem&acc=D001280&view=disease

–b) Pathways

http://ctdbase.org/detail.go?type=chem&acc=D001280&view=pathway

–c) GO terms

http://ctdbase.org/detail.go?type=chem&acc=D001280&view=go

–d) Chemicals with comparable sets of interacting genes

http://ctdbase.org/detail.go;jsessionid=DC2E24E07FFEC3BAE361C81FE7ABBBB8?type=chem&acc=D001280&view=similarActor