Computational tools and Interoperability in Comparative ... - CBS

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Danmarks Tekniske Universitet AFI, Ph.d.-uddannelse September 2005 Ph.d.-studerendes navn: Peter Fischer Hallin Cpr.-nr.: 160877 2053 Studiets hovedemne: The goal of this project is to obtain better understanding about the structural mechanisms that are involved in the initiation of transcription of DNA in Prokaryotic genomes and to use this information to make better and consistent transcript predictions. We have presented a database (Hallin and Ussery 2004) which holds several kinds of information for each of the over 300 fully sequenced Prokaryotic genomes that are currently available. Different research groups have made efforts to gather sequence data and analysis of the fully sequenced microbial genomes that are being published. Currently we rely on the authors' annotation of genome sequences when comparative genomics are applied to our data sets. However, different authors use different tools, approaches and criteria during the annotation process. There are examples of genomes that are predicted to be 50-100% over annotated (Skovgaard et al. 2001). Once reliable and automated processes for predicting transcriptomes are established, comparative analysis can be applied on the entire collection of organisms. It is envisioned that the users of our website can interactively be able to browse any piece of DNA to look for structural properties and repeats. _________________ Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A On the total number of genes and their length distribution in complete microbial genomes (2001) Trends Genet.17:425-8. Peter F. Hallin and David W. Ussery CBS Genome Atlas Database: A dynamic storage for bioinformatic results and sequence data (2004). Bioinformatics 20:3682-3686. (Her beskrives den videnskabelige projektdels indhold samt mål og midler. Hvis beskrivelsen er på mere end 1 A4side gives en kort oversigt her med henvisning til selve beskrivelsen, der vedlægges som bilag). Det eksterne forskningsophold Professor Craig John Benham, University of California, Davis. Benhams research focuses on mathematical modelling of DNA destabilization and prediction of opening of the DNA molecule during a transcription event. His strong mathematical approach is novel and would contribute significantly to our prediction methods and could possibly help explaining biological / experimental results. It is the idea that Craig Benhams calculations will be integrated into the prediction algorithms that is a major topic of my project. A 12 weeks internship is scheduled for October-December to Craig Benhams lab to integrate SIDD predictions (Stress Induced DNA Duplex Destabilization) with CBS databases and to prepare 1-2 manuscripts on SIDD measures on a global prokaryotic scale. 2
Danmarks Tekniske Universitet AFI, Ph.d.-uddannelse September 2005 Ph.d.-studerendes navn: Peter Fischer Hallin Cpr.-nr.: 160877 2053 (Her anføres de forskningsmiljøer uden for DTU, hvor den ph.d.-studerende planlægges at opholde sig. Er der indgået konkrete aftaler, anføres dette. For hvert ophold angives det skønnede tidsforbrug (f.eks. i uger), og det samlede tidsforbrug til eksterne ophold anføres). Kursusdelen: Kurser på DTU Eksterne kurser Kurser meritoverført i forbindelse med indskrivning: Biological Sequence Analysis PhD 12 ECTS [OK] 27802 Metabolic Engineering and Systems biology PhD 5 ECTS F1A 27725 Globale regulatoriske netværk i mikroorganismer MSc 5 ECTS F2B 27617 Protein structure and computational biology Msc 5 ECTS F5A 27041 Introduction to Systems Biology Msc 5 ECTS E3A For kurser, som ikke findes i studiehåndbogen, skal der vedlægges en beskrivelse af det faglige indhold. Her anføres studiets forventede kursus/uddannelsesaktivteter. For hver del angives det skønnede antal ECTS-point, der sammenlagt skal svare til ca. 30 ECTS-point. 30 ECTS-point svarer til ca. 840 timers arbejde). Formidlingsdelen ( inkl. pligtarbejde): I have spent a total of about a month's time preparing and assisting in computer exercises for the CBS course Comparative Microbial Genomics and Taxonomy (Petropolis, Brazil, Aug. 2006, http://www.cbs.dtu.dk/courses/brazilworkshop) and in preparing and giving talks at several meetings. Exercises in course ”Biological Sequence Analysis” (CBS –DTU) 1 hrs. Presentation, Modern computer tools for the biosciences (Uppsala, Sweden) Presentation: Embrace workshop on bioinformtics of Immunology (CBS – DTU) Presentation: Web Services implementation on CBS: Third Anual General Meeting of EMBRACE, (Lyon France). I plan to put in an additional month of work for giving and preparing presentations and lectures for a one week workshop to be 3
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Peter Fischer Hallin | 2009 Peter F
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Preface This Ph.D. thesis is writte
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thesis, the work is just being publ
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ved at blive publiceret i Standards
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Paper VI [Lagesen K, Hallin P] 1 ,
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3.3.3 Refining E. coli and Shigella
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xviii 2.17 Pan- and core-genome plo
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Chapter 1 Introduction Introduction
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Chapter 2 Comparative Genomics 2.1
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Comparative Genomics the publicly a
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Comparative Genomics source CDS tot
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Comparative Genomics 1 mysql -N -B
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Listing 2.8: R code to generate a 2
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1st U C A G U 2nd position C A G 3r
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1st U C A G U 2nd position C A G 3r
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Escherichia coli strain K-12, subst
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Comparative Genomics
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3M 2.5M 3.5M 2.5M 2M 0M 2M 0.5M B.
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Streptococcus Escherichia Bacillus
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2.4 Summary Comparative Genomics Th
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Comparative Genomics 2.5 Instant in
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‘ReSourCe is he best online submi
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up to a total of 41 different E. co
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Fig. 2 Genes (or segments) from eac
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Fig. 5 BLASTatlas of Clostridium bo
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different applications, such as ide
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1 Comparative Genomics 2.7 Paper II
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166 literally millions of bacterial
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168
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170 resistance genes on mobile gene
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172 involved in generating diversit
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174 recipient DNA. A feature observ
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176 Fig. 5 Genome length distributi
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178
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180 reasons why organisms remain un
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182 A final problem has to do with
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184 Middendorf B, Hochhut B, Leipol
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1 Comparative Genomics 2.8 Paper II
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2 O. N. Reva et al. Fig. 1. Genome
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4 O. N. Reva et al. decrease of the
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6 O. N. Reva et al. of which are kn
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8 O. N. Reva et al. compiled into a
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10 O. N. Reva et al. encoded by a c
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12 O. N. Reva et al. systems and ef
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1 2.9 Paper IV: The origins of Vibr
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phylogenies based on alternative ho
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Figure 1 Phylogenetic tree of the 1
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25000 20000 15000 10000 5000 0 Pan
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Gap F 2M 2.5M Gap E 875k 750k 625k
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Table 2 A selection of genes locate
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Open Access This article is distrib
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1 Comparative Genomics 2.10 Paper V
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4314 74 Tools Abstract: Of the plet
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4316 74 Tools Size distribution of
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4318 74 Tools Genome atlas Intrinsi
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4320 74 Tools Genome atlas Intrinsi
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4322 74 Tools for Comparison of Bac
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4324 74 Tools for Comparison of Bac
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4326 74 Tools information, as genet
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Chapter 3 rRNA operons and promoter
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tuB murI Fis III Fis II Fis I UP -3
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Bits 2.0 1.5 1.0 0.5 0.0 Bits 2.0 1
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Page 164 and 165: ing platform-‐independent Java
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Page 178 and 179: Chapter 5 Conclusion and perspectiv
Page 180 and 181: Appendix A Appendix: Workshops, tea
Page 182 and 183: Appendix B Appendix: Ph.D. study pl
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Page 188 and 189: Appendix C Appendix: Courses C.1 Gl
Page 190 and 191: D.2 Sample output from queryGenomes
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Page 196 and 197: Appendix: Software 25 [ ] A l t e r
Page 198 and 199: BIBLIOGRAPHY J. Rogers, P. F. Stadl
Page 200 and 201: BIBLIOGRAPHY Q. Jin, Z. Yuan, J. Xu
Page 202 and 203: BIBLIOGRAPHY Velicer, F.-J. Vorholt
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