生物信息学的新理解Bioinformatics = Data + Algorithm.pptx

我眼中的生物信息学 Bioinformatics = Data + Algorithm Bioinformatics Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data. --NIH Bioinformatics Definition Committee The Central dogma A G C T A G C U ARNDC EQGHI LKMFP STWYV Primary database • NCBI GenBank /USA • EMBL-EBI resource /EU • DDBJ /Japan NCBI Entrez interface /gene/3630 >gi|631226408|ref|NP_001278826.1| insulin preproprotein [Homo sapiens] MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREA EDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN The “Big” Data • From 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months /genbank/statistics DNA Sequencer IBM transistor sequencer CryoEM Mass Spec The Central Dogma in 21st century Secondary database • UCSC database • GPCR database Database search “alignment” • Longest Common Subsequences • Smith-waterman algorithm • heuristic search (BLAST, BLAT, Burrows- Wheeler Aligner, etc) Sequence 1 = A--CACACTA Sequence 2 = AGCACAC-A Hidden Markov Model • GenScan • Pfam/HMMER LGC HGC A 0.4 C 0.1 G 0.1 T 0.4 A 0.05 C 0.4 G 0.5 T 0.05 0.01 0.1 0.99 0.9 Data mining in biological data Human genetic study -- a case study • Background – SNP (biomarker) • Candidate-gene based study – HIV opportunistic infection • Whole genome wide study – Hepatitis C SNP (single nucleotide polymorphism) • Definition – DNA sequence variations that occur when a single nucleotide (A,T,C,or G) in the genome sequence is altered • Common human variation – 11 million (MAF>=1%) – SNP frequency varies in different population • 1000 genome project – Genotyped 25 population, ~2500 individuals • Detected method – Sequencing – PCR-based methods – Chip (Illumina, Affy) – … SNP detection Genotyping platform on Chip • Affy – Genome-wide Human SNP array 6.