![Microbial Genome Sequencing
• JGI – IMG [http://img.jgi.doe.gov/]
• Broad [http://www.broadinstitute.org/]
• TIGR [http://www.jcvi.org/]
• WashU [http://genome.wustl.edu/]
• VBI at Virginia Tech [www.vbi.vt.edu]](https://image.slidesharecdn.com/lecture-34-121208005639-phpapp01/85/Lecture-3-4-11-320.jpg)
Lecture 3,4
- 1. Genome Sequencing Projects, Genome Size, Application of sequence information for identification of disease genes
- 2. Complete Genome Sequencing Whole genome shotgun sequencing BAC end sequencing Chromosome walking End sealing
- 4. Cost of Genome Sequencing
- 5. Nextgen sequencing methods 454 sequencing methods(2006) Principles of pyrophosphate detection(1985, 1988) Illumina(Solexa) Genome sequencing methods(2007) Applied Biosystems ABI SOLiD System(2007) Helicos single molecule sequencing(Helioscope, 2007) Pacific Biosciences single-molecule real-time(SMRT) technology, 2010 Sequenom for Nanotechnology based sequencing. BioNanomatrixnanofluidiscs RNAP technology http://www.ncbi.nlm.nih.gov/books/NBK20261/
- 6. Sequencing methods http://www.wellcome.ac.uk/Education-resources/Teaching-and- education/Animations/DNA/WTDV026689.htm Ref: http://www.wellcome.ac.uk/Education-resources/Teaching-and- education/Animations/DNA/WTX056046.htm http://www.wellcome.ac.uk/Education-resources/Teaching-and- education/Animations/DNA/WTX056051.htm
- 7. Ion Torrent
- 10. http://www.insdc.org/ http://www.ebi.ac.uk/embl /Contact/collaboration.ht ml
- 11. Microbial Genome Sequencing • JGI – IMG [http://img.jgi.doe.gov/] • Broad [http://www.broadinstitute.org/] • TIGR [http://www.jcvi.org/] • WashU [http://genome.wustl.edu/] • VBI at Virginia Tech [www.vbi.vt.edu]
- 12. Human Genome Project NHGRI Solicited RFAs were First pilot sought for Publicati proposal for full on in ENCODE ENCODE 2000 In October GWAS - Finished 90% lies First Report 1990 Human ENCODE paper in outside on Encode Genome coding published 2003 Published in project started 2005 2012 2007
- 13. What happens next? You have 10 million characters – what to do with them? Locate genes Determine the function of the gene By similarity search By domain search By Predicting signal peptide By locating transmembrane region Ref: http://www.nature.com/nature/journal/v406/n6797/pdf/406799a0.pdf
- 14. Genome Annotation Run 6 frame Run Blastp ATGAAGATAGACAG translation with nr CATACTAGCAGCAT AGAATAGATAAGAG ATAGAAATAGAATA Matc h AATATAAGAGAGA found N o Repeat Finding, miRN Product found A Make an finding, tRNAs hmmsearch can etc. N O Pathway analysis Matc Other analysis h found Unknown Genes Hypothesis
- 15. Genome Sizes Gametic Nuclear DNA content Represented as mass in pg(pico grams) or length in mega bases 1 pg = 10^-12 gms 1mb = 10^6 bases 1 pg = 978 Mb Ref: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669731/
- 16. Genome Sizes Database of Genome Sizes http://www.cbs.dtu.dk/databases/DOGS/ Plant Genome database http://www.kew.org/genomesize/homepage.html Mamalian genome size database http://www.unipv.it/webbio/dbagsdb.htm Animal Genome size database www.genomesize.com Fungal Genome size database. www.zbi.ee/fungal-genomesize
- 22. Identifying Human Disease genes ref: http://www.ncbi.nlm.nih.gov/books/NBK7561/ Before 1980, very few genes were recognized Reverse Genetics: Know gene product and go back to gene and do a positional cloning Genetic Redundancy: Multiple genes have the same function
- 23. Identification of genes through protein product
- 24. 1000 genomes project 1092 genomes of different individuals sequenced. 14 populations Low coverage exome sequencing 38 million SNPs 1.4 million short insertions 14,000 large deletions Ref: http://www.nature.com/nature/journal/v491/n7422/full/nature11632.html