Index

*-character : 5.1

ADS : see aligned dual sequence

AFH : see atomic fault hypotheses

algorithms : banded dynamic programming( | banded dynamic programming)

n, m recursive look-ahead : 7.4.2.2

design techniques : 10.2

DNA-Shift-AND : 7.2.3 to 7.2.3.1

dynamic programming : 5.1 | 7.2.2

parametrising : 7.3.2

fast fourier transform : 7.2.2

greedy : 7.4.2.1

heuristic string searching : 7.2.2

optimal mismatch : 7.2.2

read extension : 7.7.2

requirements : 10.1

string comparison : 7.2.2

window search : 7.7.2

ZEBRA : 7.2.4 to 7.2.4.3

aligned dual sequence : 7.3.4 | 7.7.2

alignment : 5.1

calculation : 5.1

coverage : 5.1 | 7.4.1 | 7.6.3

expected score : 7.3.2

global : 5.1 | 7.2.2

k-tuple : 5.1

local : 5.1 | 7.2.2 | 7.3

matrix : 5.1

optimal : 7.4.3

optimality : 6.2.1

quality : 7.3.3

score : 5.1 | 7.3.2

score ratio : 7.3.3

SCS : 5.1

weight : 7.3.3

alphabet : 5.1

IUPAC : 5.1

representations : 5.1

area pooling : 7.1

assembler

comparison : 8.1

GAP4 : 8.1

integrated assembler-editor strategy : 6.2

MIRA : 8 | 8.1

PHRAP : 6.1 | 8.1

strategies : 6

strategy : 4.3

assembly

layout : 7.3.4 | 7.6.3

projects : 8.1

atomic fault hypotheses : 7.5

automatic editor : 4.3 | 6.2.2 | 7.4.4.3 | 7.5

strategy : 7.5

base

confidence value : 4.2

dideoxynucleotide termination : 5.1

extraction : see base-calling

probability : 4.2 | 5.2.1 | 7.4.4.3

quality : 4.1 | 5.2.1 | 5.2.1

base-calling : 5.1

alternative : 7.4.4.3

errors : 5.2.1

PHRED : 5.2.1

block-indel model : 7.3.2

building blocks : see read

chimera : 5.2.2 | 7.4.2.1

clipping

quality : 7.1

sequencing vector : 7.1

splice variants : 7.1

complement

base : 5.1

complexity

banded dynamic programming : 7.3.1

DNA-Shift-AND : 7.2.3

dynamic programming : 5.1 | 7.2.2 | 7.3.1

consensus

constraints : 7.4.4.1

errors : 7.4.1

sequence : 7.4.1

contamination : 5.2.2

contig : 6 | 7.4.3

building : 7.4

anchor : 7.4.1

anchor point : 7.4.3

iterative approach : 7.4

result : 7.4.1

starting point : 7.4.1

strategies : 7.4.1

minimum number : 7.3.4

object : 7.4.3

quality improvement : 7.8

read acceptance : 7.4.3 | 7.4.4

read rejection : 7.4.3

coverage : see alignment

cross_match : 8.1

cytochromes : 5.3.2.1

data

burst : 7.2.4.1

speculative prefetch : 7.2.4.1

distribution

bias : 5.1

random : 7.2.4.1

uniform : 5.1 | 7.6.2

DNASAND : see algorithms

dye

termination : 5.1

dynamic programming : see algorithms

EdIt : see automatic editor

electrophoresis : 5.1

endgaps : 5.1

exon : 5.3.1

expert system : see automatic editor

fast fourier transform : see algorithms

finishing : 4.2

fuguization : 6.1

gap

character : see *-character

penalty function : 7.3.2

genome : 5.1

graph

edge : 7.3.4

look-ahead : 7.4.2.2

node : 7.3.4

number of edges : 7.4.2

searching : 7.4.1

weighted : 7.3.4

hash

calculation : 7.2.4.1

distance : 7.2.4.1

distance histogram : 7.2.4.1

imprint : 7.2.4.1

index table : 7.2.4.1

position : 7.2.4.1

HCR : see regions

hidden data : 7.1

histogram : 7.2.4.1

Human Genome Project : 4.3

imprint : see hash

indel : 5.2.1 | 5.2.2

insert : 5.1

intron : 5.3.1

IUPAC : see alphabet

layout : see assembly

LCR : see regions

Levenshtein distance : 7.2.3

matrix

score : 5.1 | 7.3.2 | 7.3.2

weight : 5.1 | 7.3.2 | 7.3.2

micro-satellites : see repeat

MIRA

acronym : 8

misassembly

detection : 7.6.3

prevention : 7.6.3

NP

complete : 5.1

hard : 5.1

optimal mismatch : see algorithms

overlap

detection : 7.2

pattern analysis : see repeat

PHRAP : see assembler

PHRED : see base-calling

plasmid : 5.1

point mutation : 5.2.2

polybase

poly-A / poly-T uncovering : 7.1

possible repeat marker base : see repeat

PRMB : see repeat

read : 5.1

building block : 7.4.4

chimeras : 7.4.2.2 | 7.4.4.1

extension : 7.7

algorithm : 7.7.2

extra-contig : 7.7.1

intra-contig : 7.7.1

fast scanning : 7.2

region

error : 7.5

low confidence (LCR) : 7.7.1

single-base error : 7.4.4.2

regions

hidden data : 7.7

high confidence (HCR) : 6.2 | 7.1 | 7.7

low confidence (HCR) : 7.1

low confidence (LCR) : 6.2

regular expressions : 7.2.1

repeat

in graphs : 7.4.1

long : 7.6.1

micro-satellites : 7.6.1

pattern : 7.6.3

pattern analysis : 7.6.3

PRMB: possible repeat marker base : 7.6.3

recognition : 7.6 | 7.6.2 | 7.6.3

short : 7.6.1

standard elements : 7.4.4.2

standard types : 6.2.2

types : 7.6.1

restriction enzyme : 5.1

Sanger

nucleotide labelling : 5.1

scaffolding : 6.1

score

alignment : 5.1

column : 5.1

of two bases : 5.1

ratio : 7.3.3

score matrix : see matrix

sequence : 5.1

comparison : 7.2.4.1

contamination : 5.2.2

definition : 5.1

error rate : 4.1

extended length : 5.1

length : 4.1 | 5.1 | 5.1

quality : 5.2.1

quality improvement : 7.8

sequences

comparing : 7.2.4.1

sequencing vector : 7.1

Shift-AND : see algorithms

shotgun method : 5.1

signal

base extraction : see base-calling

fluorescence detection : 5.1

quality : 5.2.1

quality measures : 7.5

shape information : 7.4.4.3

signal-to-noise ratio : 7.7

trace : 5.1 | 7.4.4.3 | 7.5

translation : see base calling

signal analysis : 7.4.4.2 | 7.4.4.3

advantages : 4.3

black box : 7.4.4.3

singlet : 7.5

SNP : 5.2.2

sonication : 5.1

splicing : 5.3.1

template

constraints : 7.4.4.4

sequencing : 7.4.4.4

trace : see signal

vector

cloning : 5.1

sequencing : 5.1

weight matrix : see matrix

ZEBRA : see algorithms

Curriculum Vitae
	Particulars
	Name:	Bastien Chevreux
	Date of birth:	05.07.1972
	Nationality:	french
	Place of birth:	Duisburg, Federal Republic of Germany
	Marital status:	single
	Parents:	Bernard Chevreux
		Lydia Chevreux (born Simon)
	Schooling
1978 - 1979	Grundschule Duisburg Duisburg, Federal Republic of Germany Primary school: first class
1979 - 1983	Deutsche Schule Brüssel Brussels, Belgium Primary school: second to fourth class Comprehensive secondary school: fifth class
1983 - 1991	Gymnasium Thomaeum Kempen Kempen, Federal Republic of Germany Comprehensive secondary school: 6th to 13th class
June 12th, 1991	Gymnasium Thomaeum Kempen Kempen, Federal Republic of Germany General qualification for university entrance (Abitur)
	University
Summer term 1992	Universität Heidelberg / FH Heilbronn Heidelberg / Heilbronn, Germany Start of university studies in Medical Informatics
April 13th, 1994	Intermediate diploma
March 1st, 1997	Diploma of the University of Heidelberg in Medical Informatics