生物信息学1-NCBI使用

Alzheimer Diseaห้องสมุดไป่ตู้e
疾病名称 疾病特征
简述
临床特征
图谱定位
分子遗传学
群体遗传学
结论
从孟德尔在线，我们找到Alzheimer Disease 3的致病基因PSEN1
任务
1. PSEN1的最新研究进展 2. 对PSEN1进行序列分析
检索文献
"Alzheimer Disease 3" AND "PSEN1"
Forward primer CGGGGTCCGCGGTTTCACAT Reverse primer GCACAGCAACTTCCGGGCCT
3.Primer annealing temperature
10. Avoid Template secondary structure : A single stranded Nucleic acid sequences is highly unstable and fold into conformations (secondary structures). The stability of these template secondary structures depends largely on their free energy and melting temperatures(Tm). Consideration of template secondary structures is important in designing primers, especially in qPCR.
第三
GC CLAMP GC CLAMP
Forward primer CGGGGTCCGCGGTTTCACAT Reverse primer GCACAGCAACTTCCGGGCCT
Oligo 6 的评估
Excessive difference between product and primer melting temperatures.
NCBI
使用指南
Find genes associated with a phenotype or disease
OMIM ® - Online Mendelian Inheritance in Man ®
找到与表型和疾病相关的基因
维克多麦金西克（1921至2008年）被广泛 认为是医学遗传学的奠基人。一个创新的 临床医生，医学教育家和研究员，他于 1957年在约翰霍普金斯大学建立了第一个 医学遗传学方案和临床，构思并编写了 《人类孟德尔遗传学》，1966年出版的第 一个人的表型（每年更新的目录，现在在 网上公布） ，并在阿米什人上进行了遗传 疾病上具有里程碑意义的研究，他是一个 绘制人类基因组的早期倡导者，密切在人 类基因组计划所涉及的最初几年，作为人 类基因组组织（HUGO）的创始总裁。 1997 年他收到医学科学特别成就奖终身贡献的 拉斯克奖。
http://www.refman.com/
新建数据库
导入参考文献
设置PubMed滤器
RM/EndNote必须的格式
实现了网络和本地的数据连接
导入RefMan
序列分析
• 解读人的PSEN1基因
基因组、转录本，产物 Try our new Sequence Viewer
The guidelines for qPCR primer design vary slightly. Software such as AlleleID and Beacon Designer can design primers and oligonucleotide probes for complex detection assays such as multiplex assays, cross species primer design, species specific primer design and primer design to reduce the cost of experimentation.
7. Repeats : A repeat is a di-nucleotide occurring many times consecutively and should be avoided because they can misprime. For example: ATATATAT. A maximum number of di-nucleotide repeats acceptable in an oligo is 4 dinucleotides.
See PSEN1 in MapViewer
看改 到变 更标 宽尺 泛的 的度 失量 业范 围 ， 可 以
点击FASTA格 式，可以下载 该重叠群
SNP
基因互做
表型与基因型
Linkage Disequilbrium (LD) Analysis
选择双序列比对
Forward primer CGGGGTCCGCGGTTTCACAT Reverse primer GCACAGCAACTTCCGGGCCT
6. Primer Secondary Structures : Presence of the primer secondary structures produced by intermolecular or intramolecular interactions can lead to poor or no yield of the product.
8. Runs : Primers with long runs of a single base should generally be avoided as they can misprime. For example, AGCGGGGGATGGGG has runs of base 'G' of value 5 and 4. A maximum number of runs accepted is 4bp. 9. 3' End Stability : It is the maximum ΔG value of the five bases from the 3' end. An unstable 3' end (less negative ΔG) will result in less false priming.
可变剪切
• 设计引物的最简易方案
Pick Primers
最佳引物的评估
Forward primer CGGGGTCCGCGGTTTCACAT
Reverse primer
GCACAGCAACTTCCGGGCCT
Primer Premier 6 支持通过Entrez读取NCBI的数据 这是PP6新增的第一个功能：Automatic Sequence Retrieval
11. Avoid Cross homology : To improve specificity of the primers it is necessary to avoid regions of homology. Primers designed for a sequence must not amplify other genes in the mixture. Commonly, primers are designed and then BLASTed to test the specificity.
综述60篇 总共335篇，其中 免费全文83篇
选择摘要显示，以便快速阅读
选择MEDLINE显示，以便存储参考文献
启动 Reference Manager 12
ReferenceManager是美国Researchsoft公司开发的一个文献管理与检索软件， 是一个专门设计来管理书目参考文献的资料库程序。任何需要收集参考文献做研 究之用或需要制作书目的人都可以使用ReferenceManager更轻易地管理资料。 实际上，ReferenceManager在全球很多学术机构以及商业、研究机构的研究人 员、图书馆员和学生中都有着广泛地使用。
• 在BLAST PRIMER里面最好的引物，在PP6里 却是评分得到了一个“POOR”；而在oligo6 里面评估却是无法扩增。
o(︶︿︶)o 唉
PCR Primer Design Guidelines
1. Primer Length: It is generally accepted that the optimal length of PCR primers is 18-22 bp. This length is long enough for adequate specificity, and short enough for primers to bind easily to the template at the annealing temperature. 2. Primer Melting Temperature: Primer Melting Temperature (Tm) by definition is the temperature at which one half of the DNA duplex will dissociate to become single stranded and indicates the duplex stability. Primers with melting temperatures in the range of 52-58 oC generally produce the best results. 4. GC Content : The GC content (the number of G's and C's in the primer as a percentage of the total bases) of primer should be 40-60%. 5. GC Clamp : The presence of G or C bases within the lat five bases from the 3' end of primers (GC clamp) helps promote specific binding at the 3' end due to the stronger bonding of G and C bases. More than 3 G's or C's should be avoided in the last 5 bases at the 3' end of the primer.
Quickly retrieves batches of sequences directly into the program from GenBank and dbSNP using accession/GI numbers and assay Ids. Using the multiple retrieval facility, sequences can be loaded from local drives.
PP6新增的第三个功能： Evaluate Pre-designed Primers Primer Premier analyzes and evaluates the properties of pre-designed primers and ranks them for you to adjudge how far the primers are from their desired target values. This feature is especially useful if you are working with published or pre-designed well proven primers.