Exam Review material to be covered from

Why Bioinformatics and Genome Analysis Eric Greene talk and handouts Biological Information DNA RNA proteins ACTG Exercise 1 online biological info access NCBI and NHGRI Bioinformatics of Sequencing Sanger, EBI and why the human genome Gene detection and genome annotation: Onconomics corporation, contigs
Sequence alignment and BLAST Baxevantis talk and BLAST

DNA Microarray analysis RNA transcription Lecture Examination # 1 Sequenced genomes and the human genome project SNPs and Genome Wide association Genetic variation exercises Proteins and Proteomics

The exam will focus on your knowledge of the tools you have used in the exercises and in class to evaluate your understanding of how these tools will help address biological problems
1.

What is bioinformatics-?

Extraction of biological knowledge from complex data

What is the human genome project? 13-year international effort to sequence all 3 billion base pairs in human DNA and identify all human genes. The project was completed in 2003. Other goals included sequencing genomes of model organisms, developing technology for research, exploring gene functions, studying variation in humans, and training future scientists.
2.

Sanger sequencing

Sanger dideoxy sequencing. This process takes advantage of the ability of DNA polymerase to incorporate 2, 3-dideoxynucleotides, nucleotide base analogs that lack the 3-hydroxyl group essential in phosphodiester bond formation. . Sanger dideoxy sequencing results in the formation of extension products of various lengths terminated with dideoxynucleotides at the 3 end
3.

Use of OMIM, use of Pubmed when and why would you use it? OMIM- focus on the molecular relationship between genetic variation and phenotypic expression. used as excellent resource to use to gain a better overall understanding of a disease or gene

PubMed- search engines useful in literature searches

4.

What are three reasons for sequencing entire genomes? *convert data to knowledge *generate new hypotheses *Design new experiments

5.

Explain the need for bioinformatics and progress in sequencing technologies that are important for Genomics. Given the availability of: Bacterial artificial chromosome (BAC) libraries- promotes ease in chromosome mapping and analysis of the human genome gel electrophoresisrestriction enzymesDNA hybridization-PCR High throughput DNA sequencing Computer programs for interpreting massive amounts of DNA sequence data

Describe how you would sequence an entire genome leading to:

Complete genome sequence with a minimum number of gaps Very high quality sequence with fewer than 1 error per 10,000 bases Likely locations of known and predicted genes The lowest cost possible

Please write your answer as a numbered list of the steps that you would follow, highlighting the reasoning and expected results from each step. Define Genome- an organisms complete set of DNA, including all of its genes. Transcriptiome- collection of all the transcripts present in a given cell Proteome- protein complement of an organism coded for by its genome. Genomics: study of genomes on large scale Transcriptomics: study of gene expression on large scale Proteomics: study of proteins on large scale

ELSI- Ethical, Legal and Social Implications Describe the sequencing of the human genome why is the genomics effort important? The work of the Human Genome Project has allowed researchers to begin to understand the blueprint for building a person. As researchers learn more about the functions of genes and proteins, this knowledge will have a major impact in the fields of medicine, biotechnology, and the life sciences. 2 What is the importance of sequence analysis? ie what kinds of questions are we trying to answer through sequence analysis. Describe two bioinformatics tools/databases? Sequence analysis can be used to assign function to genes and proteins by the study of the similarities between the compared sequences. Bioinormatics tools/databases= PubMed & GenBank 3 What are NCBI: National Center for Biotechnology Information NHGRI: National Human Genome Research Institute EBI: European Bioinformatics Institute

5.

Give four examples of sequenced genomes

Short definitions, matching and opinion

1965 Margaret Dayhoff's Atlas of Protein Sequences