Biologically m eaningful cl assification o f pro teinsequences – a b ioinformatic approachder Fakultät für Biologieder E berhard Kar ls Uni versität Tü bingenzur Erlangung des G rades ei nes Doktorsder N aturwissenschaftenvonTancred Gil les Fr ickeyaus New Yo rkvorgelegteD i s s e r t a t i o n2005Tag der mündlichen Prüfung: 20.07.2005Dekan: Prof. Dr. Friedrich Schöffl1. Berichterstatter: Prof. Dr. Andrei Lupas2. Berichterstatter: Prof. Dr. Alfred NordheimTable of contents:Curriculum V itaeAbstract (German)Introduction: 1Aligning two sequences 2Finding sequence relatives 3Phyl ogenetic tree construction 4Bo otstrapping 8Suboptim al alignment 10 and mutational saturationEvolution, lateralgene transfer 11 and genome duplicationProt ein classification 14Aim 16Results and Discussion: 18 Project I: PhyloGenie 18 II: Alignment validation 19 Project III: CLANS 20 IV: Phylogenetic analysis of AAAproteins 21Contribution: 23Appendix: 25BLOSUM62 substitution matrix 25Phyl oGenie: automated phylome generationand analysis.C LANS: a Java application for visualizing protein families based on pairwise similarity.Phyl ogenetic analysis of AAAproteins.Bibliography: IIII Curriculum V itaeName: Tancred Gill es F rickey Birth: 28.08.74 in New Y orkAddress: Vöchtingstr. 0 972076 Tu ebingen, G ermanyTelephone: +49 (0) 7071 6 01342 ( work)Father: Franklin William F rickey ( 09.
Biologically meaningful classification of protein sequences – a bioinformatic approach
der Fakultät für Biologie der Eberhard Karls Universität Tübingen
zur Erlangung des Grades eines Doktors der Naturwissenschaften
von
Tancred Gilles Frickey aus New York
vorgelegte D i s s e r t a t i o n 2005
Tag der mündlichen Prüfung:
Dekan:
1. Berichterstatter:
2. Berichterstatter:
20.07.2005
Prof. Dr. Friedrich Schöffl
Prof. Dr. Andrei Lupas
Prof. Dr. Alfred Nordheim
Table of contents: Curriculum Vitae Abstract (German) Introduction: -Aligning two sequences -Finding sequence relatives -Phylogenetic tree construction -Bootstrapping -Suboptimal alignment and mutational saturation -Evolution, lateral-gene transfer and genome duplication -Protein classification -Aim Results and Discussion: - Project I: PhyloGenie - Project II: Alignment validation - Project III: CLANS - Project IV: Phylogenetic analysis of AAA-proteins Contribution: Appendix: -BLOSUM62 substitution matrix -PhyloGenie: automated phylome generation and analysis. -CLANS: a Java application for visualizing protein families based on pairwise similarity. -Phylogenetic analysis of AAA-proteins. Bibliography:
1 2 3 4 8 10 11 14 16 18 18 19 20 21 23 25 25
I-III
Curriculum Vitae Name: Tancred Gilles Frickey Birth: 28.08.74 in New York Address: Vöchtingstr. 09 72076 Tuebingen, Germany Telephone: +49 (0)7071 601342 (work)
Father: Franklin William Frickey (09.07.42) Mother: Genevieve Marie Frickey (11.01.43)
Personal: Unmarried US and French nationality Languages: German (fluent), English (fluent), French (fluent) Computer skills: Languages: Java, Perl, HTML OS: Windows95/98/2000/NT4, Solaris, Linux
Education: 2001-2005 Ph.D.student: Max-Planck Institute for Developmental Biology, Tübingen “Biologically meaningful classification of protein sequences – a bioinformatic approach.” 2001 Diploma: Biology, Constance University “Dealing with mutational saturation at the amino acid level” 1996-2001 Biology, Constance University WS 1995 Cybernetics, Stuttgart University 06.1994 (Baccalaureat) Abitur Kaiserin-Friedrich-Gymnasium Majors: English, Chemistry 1985-94 Kaiserin-Friedrich-Gymnasium 1981-85 Grundschule Ober-Erlenbach
Professional experience: 10.2001-present Ph.D. student: MPI for Developmental Biology SS 1997-WS 2001 Student assistant in the Workgroup Meyer Evolutionary Biology, Constance University 08.07.96-04.08.96 Practical at Sanitätshaus Reininger Construction of Prosthetics-, Orthetics 01.06.96-01.07.96 Practical at the architectural design firm Barsties 10.07.95-04.08.95 Practical at ITT Automotive Europe Gmbh (Lathe, milling machine) 04.10.94-10.07.95 National service (France)