Bioinformatics Educated by Zhenglin Zhu School of Life Sciences, Chongqing U.

For Education Materials: bioinformatics/  Brief introduction to bioinformatics  Linux  Basic orders and management  Bash Programming  Sequence Alignment  Basics of sequence alignment  BLAST  EMBOSS  Biological Databases  Phylogenetic Tree  Theory  Practice to make trees using MEGA  Protein modeling  Theory  SPDBViewer  Microarray  Theory  Limma  Designing for PCR primers

Brief Introduction to Bioinformatics Zhengli Zhu, School of Life Sciences

Outline 1. What is bioinformatics? 2. What is biological data object? 3. Where to obtain biological data? 4. How to deal with biological data? 5. Start your career as a bioinformatician

Bioinformatics is the storage, management and analysis of biological data. Biological Data StorageManagementAnalysis

Outline 1. What is bioinformatics? 2. What is biological data object? 3. Where to obtain biological data? 4. How to deal with biological data? 5. Start your career as a bioinformatician

History Cited form“Wikipedia – Central dogma of molecular biology” 1986 提出计划 研究论证 1991 开始人类基因 组计划 2000 发布人类基 因组草图 2003 完成人类基 因组测序

The era of omics Biological data DNA (Genomics) RNA (Transcriptomics) Protein (proteomics)

Outline 1. What is bioinformatics? 2. What is biological data object? 3. Where to obtain biological data? 4. How to deal with biological data? 5. Start your career as a bioinformatician

Raw data Sequencing – DNA & RNA Microarray – DNA & RNA Mass spectrography - protein Database Level 1: raw data storage Level 2: knowledge based and manually curated Reanalysis and literature mining Level 2 database Raw data Level 1 database literature User dataset Raw dataliterature Level 2 database Level 1 database

NCBI is friendly  Boolean expression query  Keyword1 AND keyword2  Keyword1 OR keyword2  Keyword1NOT keyword2  More than 20 nodes query network  Data transfer through FTP The Entrez system

While (keywords are not empty) Do { Search “new gene AND microevolution” in PubMed system; focus on “review” and “recent” papers; generate new keywords; } Basic literature mining process of new gene evolution in the form of pseudo code.

EBI is rigorous  Powerful tool development  EMBOSS  ClustalW  PICR  InterProScan  Bioconductor  Ensemble mysql interface  Well-defined tables  Perl API DNA uID Annotation … RNA uID Expression … Protein uID Structure …

Level 2 database More professional and evaluated details! In situ hybridization High throughput Deep sequencing

Outline 1. What is bioinformatics? 2. What is biological data object? 3. Where to obtain biological data? 4. How to deal with biological data? 5. Start your career as a bioinformatician

Data analysis strategy Bioinformatician: data orientated Biologist: question driven Analysis pipelines are usually generated by data-oriented tasks, while question- driven tasks demand a combination of different pipelines.

Sequence analysis sequenceFeaturesGC contentCodon usage Motif/domain recognition Secondary structure analysis Searching for similar sequences Phylogenetic analysis Data oriented

Genome analysis Genome De novo assembly annotate Comparative genomics Population genetics Resequencing Variation detection Quantitative trait locus analysis Genome wide association study Data oriented

Transcriptome analysis RNAProfiling Identification differentially expressed genes Enrichment analysis Small RNA Identify small RNAs Target prediction Data oriented

Proteomics analysis Protein Peptide mass fingerprinting Interaction identification Novel protein/peptide identification Profiling Structural proteomics Homology modeling Function infer Data oriented

The dream bioinformaticians - From data integration to system biology

Information: Drosophila Gene Age-dependent Male-biased Distribution Question driven Background: 12 Drosophila species Melanogaster as model Sex chromosome evolution Cited from

Swift thoughts  Solution  Fetch gene information from database  Find out the presence of genes in different species  Find out male-biased genes  Analyze their chromosomal distribution

Dating D. m elanogaster genes on Drosophila phylogenetic tree

Inference of gene orientation mechanism

Outline 1. What is bioinformatics? 2. What is biological data object? 3. Where to obtain biological data? 4. How to deal with biological data? 5. Start your career as a bioinformatician

Two major types of bioinformatics guys Work as a data analyst? Or dedicate yourself to biological questions?  You should be familiar with different type of biological data and capable of dealing with them in any way  Strong computer skills  Play biosoftwares  Experts in Linux  Very familiar with at least one programming language  Know how to set up a database  Familiar with algorithms and able to generate models  The most important thing is sophisticated understanding of biological concepts  Basic computing skills  Comfortable to work in Linux  Able to write scripts  Maybe some wet experimental skills  PCR  Cloning

Useful URL  Biological sources  NCBI  EBI  Related labs  Our lab  CBI