麻省理工大学：《Foundations of Biology》课程教学资源（英文版）Lecture 1 Michael Yaffe Introduction to Bioinformatics

7, 91- Lecture #1 Michael Yaffe Introduction to bioinformatics Focus on Kinases pairwise Sequence Comparisons ARDE SHGLLENKLLGCDSMRWE ::::: GRDYKMALLEOWILGCD-MRWD Readi This lecture: Mount pp 1-7, 29-35, 45-48, 51-64 NeXt lecture: Mount pp 8-9, 65-89, 96-115, +more TheProteinDataBank(pdb-http://www.pdb.org/)isthesingle worldwide repository for the processing and distribution of 3-D biological macromolecular struct Berman, H M, J. Westbrook, Z. Feng, G. Gilliland, T N Bhat, H Weissig, I N. Shindyalov, and P. E Bourne. The Protein Data Bank. Nucleic Acids Research 28(2000): 235-242 (PDB Advisory Notice on using materials available in the archive http://www.rcsb.org/pdb/advisory.html

7.91 – Lecture #1 Introduction to Bioinformatics Focus on Kinases & Pairwise Sequence Comparisons ARDFSHGLLENKLLGCDSMRWE .::. .:::. .:::: :::. GRDYKMALLEQWILGCD-MRWD Reading: This lecture: Mount pp.1-7, 29-35, 45-48, 51-64 Next lecture: Mount pp. 8-9, 65-89, 96-115, +more The Protein Data Bank (PDB - http://www.pdb.org/) is the single biological macromolecular structure data. Research 28 (2000): 235-242. (PDB Advisory Notice on using materials available in the archive: worldwide repository for the processing and distribution of 3-D Research 28 (2000): 235-242. (PDB Advisory Notice on using materials available in the archive: http://www.rcsb.org/pdb/advisory.html) Michael Yaffe Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. The Protein Data Bank. Nucleic Acids Research 28 (2000): 235-242. http://www.rcsb.org/pdb/advisory.html)

Outline Review of biological fundamentals Genetics example Biological databases/NCBI resources Simplified sequence analysis- where to start Simple sequence comparisons Definitions of related sequences Concepts and types of alignments-the good the bad, and the ugly Dot matrix alignments Computational efficiency Recursion and dynamic programming Substitution matrices: PAM. bloSUM, Gonnet

Outline • Review of biological fundamentals • Genetics example • Biological databases/NCBI resources • Simplified sequence analysis – where to start… • Simple sequence comparisons • Definitions of related sequences • Concepts and types of alignments – the good, the bad, and the ugly • Dot matrix alignments • Computational efficiency • Recursion and dynamic programming • Substitution matrices: PAM, BLOSUM, Gonnet

Outline(cont) Gaps Applied dynamic programming: global alignments: Needleman-Wunsch Applied dynamic programming local alignments- Smith-Waterman Basic statistics of sequence alignments

Outline (cont) • Gaps • Applied dynamic programming: global alignments: Needleman-Wunsch • Applied dynamic programming: local alignments – Smith-Waterman • Basic statistics of sequence alignments

Review of biological fundamentals Genetic material gene as a concept DNA DNa as hereditary material RNA Protein Critical cell functions

Review of biological fundamentals Genetic material • gene as a concept DNA • DNA as hereditary material RNA Protein Critical cell functions

DNA structure A G Bases

DNA structure A G C T U Bases

DNA Structure A G NH2 ase pairing

DNA structure A G C T Base pairing

DNA Structure 5 Nucleoside Nucleotide

DNA structure 1 5 4 3 2 1 5 4 3 2 Nucleoside Nucleotide

DNA Structure

DNA structure 5’ 3’

DNA Structure

DNA structure 5’ 3’

DNA Structure

DNA structure 5’ 3’ 3’ 5’