生物信息学题目.doc

第一次课1.Please search one article via PubMED and give the abstract:Liu WY, et al. The OsDHODH1 gene is involved in salt and drought tolerance in rice. , J Integr Plant Biol. 2009 Sep;51(9):825-33 (OK)2. Please search the articles about human cancer research published before 2005.(OK)3. Please search all the articles related to rice yield, published in “Nature”.(OK)4. Please search all literatures published from 2000 to now, by authors from Nanjing Agricultural University.(OK)5. Please search all articles from your laboratory, published in 2010, and save all the abstracts in your local computer.(OK)6. Please search literatures involved in flower development, written by Dr. Zhang, after 2002.(OK) 第二次课1. Search the NR database to check the ZFP252 paralogues in rice and orthologues in other plant speciesprotein中ZFP252，直接runblast 2. Search for dbEST database to find ESTs of ZFP252, then check the sources of ZFP252 expression.(OK)3. Search for rice zinc finger proteins related article(s) in PubMED database.（OK）1.Search for rice gene ZFP252 in GenBank, give the gene length and number of amino acids; Check whether some ZFP252 articles were published. 在基因库中搜寻ZFP252，基因长度和氨基酸数目，检测文章是否发表Nucleotide中ZFP2522. Search UniGene database for rice gene ZFP252 and seek for the tissues in which ZFP252 is transcribed.UNIGENE3. See the GEO profile of ZFP252 and check what factors regulate ZFP252 expression.UGEO4. Try to download the data for salt responsive small RNA analysis in cotton and open it in Excel program.GEO DATESETSCottonorganism AND MiRNA AND salt第三次课1.Find ZFP252 protein sequence from rice;从水稻中找到ZFP252蛋白序列2.Randomly pick four ZFP252-like protein sequences from various plant species;从各种植物物种中随机选四种与ZFP252相似序列.RUNBLAST3.Multiple sequence alignment for above 4-5 sequences. Copy the alignment into Ms-Word or PPT.以上45序列序列多样性组合多序列比对1. Find rice ZFP252 sequence and use the sequence to find at least three different ZFP252-like protein sequences in different plant species. Protein ZFP252 2Find whether rice ZFP182 sequence is complete? Find at least three ESTs matching ZFP182 and show the EST sources. How many ZFP182-like members in rice genome? BLASTX找序列是否完整，找出至少三个EST相称的ZFP182，EST来源，在水稻基因组中找出与ZFP252相似成员Neclotide ZFP182复制其DNA 序列，找blast 粘贴，选择EST数据再blast3 I got a new sequence from rice as follows: GGCGCCGCTGATCGCGGCAGCGGTGGTGGCGGTGACTACGCCGGCGGCGGCCGTGGTAGTTCTAACTCCTTCGGTGGAGGCTCTGGCACTGGCTCTGATGTCCGCCCAGGTAACTGGTACTGCAACTGCGCCGCGCACAACTTCGCCAGCCGCTCCAGCTGCTTCAAGTGCGCTGCTTTCATTTAGGACGATGCTACCGTCAACAGTGGCGGCGCTGGTGCCTTTCTGGACGGTCCCGACATGTCGCGCACGCGGGGCTACGGCTTCGGCACCGGCGCCGTCCGCGCCAGCCGCCCTGGCTGGAAGTCTGGCGACTGGATTTGCACCAGGTCTGGATGCAATTAGCTTAACTTCGCCAGCACCTCAGAGTGCTTCAGGTGCAACCCGCCGGACTCCGGAAACACTGAGGTGTAATTTGCCGTACATTQuestions:1】What kind of protein is encoded by this sequence?哪种蛋白质被这个序列所编码blastn2】Is this sequence new or not?这种序列是否是新的blastn3】Is there any homologues of this sequence discovered in rice and other species? blastn4】Does this sequence contain the complete CDS/ORF?序列包含完整的CDS/ORF blastx(5)】 Are there any ESTs matching this sequence?第五次1.Search for rice ZFP252 protein sequence, predict the MW and pI(BioXM);检索水稻ZFP252蛋白序列，预测其等电点和分子量BioXM2. Subcellular localization prediction for ZFP252(ProtCOMP);预测ZFP252的亚细胞定位ProtCOMP3. Motif(Motif Scan) prediction for ZFP252;预测ZFP252的MOTIFMotif(Motif Scan4. Extract the ZFP252 promoter sequence(1800bp upstream sequence)(BLAST) 明确ZFP252的启动子序列blast5. (Optional) Cis-acting element analysis on ZFP252 promoter.(MatInspector)第六次1Find the ZFP252 protein sequence;2Find four ZFP25