Web based tools are used in each of the
workshop modules to help
interrogate biological data. The aims of each of the modules is
De novo Analysis of Sequence
- View manually annotated genes in the Vega browser.
- Sequence similarity searching using Blastn and PSI-blast to identify similar proteins.
- De novo analysis of cDNAs, including ORF finder to highlight putative protein products of a cDNA, blastp link from within this to investigate the potential protein products, Spidey to align cDNA to genomic DNA.
- Clustalw to align similar sequences, view in Jalview and use GeneDoc to produce a graphics file.
- InterPro to investigate protein domain structures.
Browsing the Human Genome
- Appreciate ability to now work with the whole genome
- Introduce primary human genome browsers
- Discuss how genome annotations are displayed and relevant information is made accessible
- Demonstrate some general features and applications of genome browsers.
- Introduction to the applications of the UCSC genome browser
- Introduction to the applications of the Ensembl
- Explore ability to view your own annotations in the browser
- Provide examples to facilitate becoming more comfortable using browser resources.
- Review the sequence available from different organismsIdentify putative homologous genes and generate a phylogenetic tree
- Compare genome sequences from different organisms and identify conserved sequences
- Analyze conserved sequences for potential regulatory function
Exploring Gene and Protein Function and Disease
- Identify information available to determine the possible function of a gene product
- Highlight various inter-linked information resources that are available for this purpose
- Identify published information on the gene
- Identify known Mendelian inherited disorder(s) associated with the gene
- Summarize predicted function from several linked databases
- Identify domains found within the protein
- Protein databases and analysis
- View structural information if available.
- Introduction to SNPs
- Introduction to various SNP resources on the web, including Ensembl, dbSNP and JSNP
- Integration of information from various databases to identify SNPs in target gene or chromosomal regions
- Export SNP information from databases
- Introduction to genotypes and haplotypes, including the HapMap database
- Introduction to genotyping low, medium and high throughput genotyping platforms and information about study design and QC
Major Bioinformatic Resources
- Introduction to GenBank
- Introduction to the Gene expression Omnibus (GEO)
- Introduction to the Short Read Archive (SRA)
- Introduction to the Database of Genotypes and Phenotypes (dbGAP)
Next Generation Sequencing
- An exploration of next generation sequencing platforms including:
- Platform description
- De novo sequence generation
- Sequence QC metrics and assembly
- Sequence Assembly via Galaxy
- RNA-Seq Analysis
- Review common array-based technologies to measure DNA and RNA
- Review common approaches to analysis
- Identify a region of chromosomal gain using Array CGH data
- Determine Genes with differential expression in region of chromosomal gain
The Human Epigenome
- Defining the field of epigenomics
- Exploring DNA methylation and histone modifications
- Methods of how to interrogate the methylome
- The use of next-generation sequencing approaches in epigenomic profiling
- Description of how to target the methylation status of genes
- Worked examples of methylation analyses
- Basics of protein chemistry
- Basics of mass spectrometry for characterization of peptides and proteins
- Common LC/MS/MS methods for protein identification
- Software tools for interpreting qualitative LC/MS/MS data
- Methods for differential expression proteomics
- Software tools for interpreting differential expression proteomics data
- Tools for placing differentially expressed proteins into signaling/regulatory pathways