Paper reading (一)：Bioinformatics: an overview and its applications

• Genetics and Molecular Research 16 (1)
• Wellison Jarles Da Silva Diniz
  Universidade Federal de São Carlos
• Key words:Data analysis; Databases; Genomics; Systems biology
  这是一篇综述：an overview of bioinformatics and its use in the analysis of biological data, exploring approaches, emerging methodologies, and tools that can give biological meaning to the data generated.
• 1.the emergence of new analytical strategies
  2.the use of genomic technologies in gene therapy and personalized medicine
  感觉结论没有什么特别的东西，大概意思就是数据生成，数据分析以及数据的解释性都取得了很大的进步，前景很好。但是也急需新的数据分析策略。另外，要求多背景的研究者，感觉能更好的去做这样问题的研究。
• 1.a large amount of “omic” data
  2.The crescent generation and availability of this information available in public databases
  3.make sense of the enormous amount of structural data and sequences
  4.development of tools is necessary (statistical and computational) capable of assisting in understanding the mechanisms underlying biological questions
  5.a highly reductionist view.
  6.bioinformatics and computational biology的出现，催生了new biology
  7.bioinformatics and genomics have evolved interdependently
  该综述主要包含：
  1.types of biological information and databases; 
  2.sequence analysis and molecular modeling;
  3.genomic analysis,
  4.systems biology. 
• 1.介绍了生物信息学的历史和概念
  2.organisation of information：types of information and databases
  3.analysis of biological sequences
  4.genome-wide analyzes-from genome to proteome
  5.system biology：the whole is greater than the sum of the parts
  文章主要就是从introduction中提到的四个方面进行阐述。
• Historical moments：
  1.the publication of the structure of DNA
  2.the accumulation of data and knowledge of biochemistry and protein structure
  BOOK:Atlas of Protein Sequence and Structure
• Regarding the issues involved in bioinformatics, we can classify them into two classes: the first related to the sequence and the second related to the biomolecular structure 
  The information sources used by bioinformatics can be divided into
   i) raw DNA sequences,
  ii) protein sequences, 
  iii) macromolecular structures, 
  iv) genome sequencing, among others.
• Public databases store big amounts of information, and they are classified into primary and secondary databases. 
  Alignment can be categorized by type according to the number of sequences that are compared, which can be: i) simple and ii) multiple.
  有各种对齐方法的列表总结
  the BLAST may be divided into four stages . 
  i) Compiling the word list (k-tuples); 
  ii) searching for correspondence in the database; 
  iii) extending alignments from the identified words,
  iv) assembling the spaced alignments according to high-score segment pairs (HSP) .
  The prediction process consists of five main steps : 
  1) reference identification;
  2) selection of templates;
  3) alignment; 
  4) construction,
  5) model validation .
• data integration emerges to link our ability to generate large amounts of data to our understanding of biology, making it possible to identify key genomic factors and their interactions that explain the biological result.