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APPENDIX C: BIOINFORMATICS GLOSSARY 293

Thymine: one of the nitrogenous bases that has a single - ring structure, classi-

ﬁ ed as a pyrimidine, found in DNA but not in RNA.

Tissue: a section of an organ that consists of a largely homogeneous popula-

tion of cell types. Since many organs are multifunctional, they have devel-

oped highly specialized cell types to perform different functions. Identifying

the section of an organ that is homogeneous for a particular cell type

ensures that the gene expression proﬁ les extracted from those cells will

accurately resemble the class of cells that make up the tissue.

Toxicology: the science of the harmful effects of chemicals (including drugs)

on living biological systems. It seeks to determine the mechanisms by which

chemicals produce adverse effects in cells and organisms.

Transcript: the single - stranded mRNA chain that is assembled from a gene

template.

Transcription: the assembly of complementary single - stranded RNA on a

DNA template.

Transcription factors: a group of regulatory proteins that are required for

transcription in eukaryotes. Transcription factors bind to the promoter

region of a gene and facilitate transcription by RNA polymerase.

Transfer RNA (tRNA): a small RNA molecule that recognizes a speciﬁ c

amino acid, transports it to a speciﬁ c codon in the mRNA, and positions it

properly in the nascent polypeptide chain.

Transformation: a genetic alteration to a cell as a result of the incorporation

of DNA from a genetically diferent cell or virus; can also refer to the intro-

duction of DNA into bacterial cells for genetic manipulation.

Translation: the process of converting RNA to protein by the assembly of a

polypeptide chain from an mRNA molecule at the ribosome.

Transposons: mobile DNA elements that insert into other chromosomal ele-

ments (also referred to as “ jumping genes. ” )

Triple helical DNA: a mostly synthetic form of DNA; it may exist during

recombination and DNA repair.

Unidentiﬁ ed reading frame (URF): an open reading frame encoding a protein

of undeﬁ ned function.

UniGene database

1,2

: a public database, maintained by NCBI, which brings

together sets of GenBank sequences that represent the transcription prod-

ucts of distinct genes.

Unique clone

1,2

: an Incyte sequence that has no match in GenBank or other

public database.

Uracil: one of the nitrogenous bases that has a single - ring structure, classiﬁ ed

as a pyrimidine, found in RNA but not in DNA.

Variable numbers of tandem repeats (VNTRs): DNA sequence blocks of

2 to 60 base pairs which are repeated from two to more than 20 times

in different individuals. This polymorphism makes VNTRs very useful

DNA markers used in genomic mapping, linkage analysis, and DNA

ﬁ ngerprinting.

294 APPENDIX C: BIOINFORMATICS GLOSSARY

Variations (genetic): variations in genetic sequences and the detection of

DNA sequence variants genome - wide allow studies relating the distribu-

tion of sequence variation to a population history. This, in turn, makes pos-

sible a determination of the density of SNPs or other markers needed for

gene mapping studies. Quantitation of these variations, together with ana-

lytical tools for studying sequence variation, also relates genetic variations

to phenotype.

Vector: any agent that transfers material (typically, DNA) from one host to

another. Typically, DNA vectors are autonomous DNA elements (such as

plasmids) that can be manipulated and integrated into a host ’ s DNA or

recombinant viruses.

Version (in GenBank)

1,2

: similar to the Protein ID for protein sequences, the

version is a nucleotide sequence identiﬁ cation number assigned to each

GenBank sequence. The format for this sequence identiﬁ er is accession.

version (e.g., M12345.1). Whenever the author of a particular sequence

record changes the sequence data in any way (even if just a single nucleo-

tide is altered), the version number will be increased by an increment of

one while the accession number base remains constant. For example,

M12345.1 would become M12345.2. Each sequence change also results in

the assignment of a new GI number (link to GI entry). Whenever an NCBI

sequence database is searched, only the most recent version of a record is

retrieved. NCBI ’ s Sequence Revision History page is used to view the

various GI numbers, version numbers, or update dates associated with a

particular GenBank record.

Virtual libraries: the creation and storage of vast collections of molecular

structures in an electronic database. These databases may be queried for

subsets that exhibit speciﬁ c physicochemical features, or may be “ virtually

screened ” for their ability to bind a drug target. This process may be per-

formed prior to the synthesis and testing of the molecules themselves.

Visualization: a process of representing abstract scientiﬁ c data as images that

can aid in understanding the meaning of the data.

Weight matrix: the density of binding sites in a gene or sequence can be used

to derive a ratio of density for each element in a pattern of interest. The

combined individual density ratios of all elements are then used collectively

to build a scoring proﬁ le known as a weight matrix. This proﬁ le can be used

to test the prediction of the identiﬁ cation of the pattern selected and the

ability of the algorithm to discriminate it from a nonpattern sequences.

X chromosome: in mammals, the sex chromosome that is found in two copies

in the homogametic sex (female in humans) and one copy in the heteroga-

metic sex (male in humans).

Y chromosome: in mammals, the sex chromosome that is found in one copy

in males and not at all in females.

Yeast two - hybrid system: a yeast - based method used to simultaneously iden-

tify, and clone the gene for, proteins interacting with a known protein.

APPENDIX C: BIOINFORMATICS GLOSSARY 295

Z DNA: a conformation of DNA existing as a left - handed double helix (the

phosphate - sugar backbone forms a left - handed zigzag course), which may

play a role in gene regulation.

REFERENCES

1. The Department of Energy (DOE) Human Genome Program . http://www.ornl.gov/

sci/techresources/Human_Genome/glossary/ .

2. National Center for Biotechnology Information (NCBI) . http://www.ncbi.nlm.nih.gov/

Education/BLASTinfo/glossary2.html .

INDEX

abstract algebra, 10

Alexander polynomial, 101

autopoiesis, 234–235, 247

networks, 235

bipolar algebra, 208–214, 218–219, 222–224

even-odd algebra, 208

Yin-Yang algebra, 208, 228

cellular automata, 235

central dogma of informatics, 249, 251, 253,

256, 258

central dogma of molecular biology, 249, 251,

253–256

centrality, 142, 144–146

eigenvector centrality, 144–145

centrality score, 146

clustering coefﬁ cient, 142–144, 147

codon, 26, 37, 58

anti-codon, 26, 37

stop-codon, 27

convex hull, 114, 135

cyclic shift, 40

diadic shifts, 25, 38, 39, 40, 53

cytology, 1

degeneracy, 26, 27, 29, 60

denotational mathematics, 229, 238–240, 248

differential geometry, 13

dissipative structure, 229, 234–236, 246–247

double helix, 3

DNA walk, 162–164

enzyme, 4

restriction enzyme, 4, 5

special enzymes, 4

Mathematics of Bioinformatics: Theory, Practice, and Applications, By Matthew He and

Sergey Petoukhov

297

Fibonacci code, 167, 169–171

ﬁ eld, 12

fractals, 15, 16, 141, 159, 160, 162–163, 173,

179

fractal dimension, 161–163, 172–173, 179

of protein surfaces, 163

fractal geometry, 157–159. 162, 173, 178–179

gene regulatory network, 137–138, 148–151,

153, 156

genetic map, 2

genomatrix, 34, 36, 43

numeric genomatrices, 41, 42, 43, 44

quint genomatrices, 47

golden genomatrices, 47

bi-symmetric genomatrices, 60

global alignment, 69, 72–73, 76, 81–82

global pairwise alignment, 70

golden matrices, 44–47

golden section, 25, 41, 43–47, 49–50, 60

graph, 12, 15

directed graph, 138–140, 143, 148, 150,

153–154

graph theory, 15

undirected graph, 138–140

weighted graphs, 138–140, 143, 148, 150,

153–154

group, 11

Hadamard matrix, 194–195, 198, 228

balanced Hadamard matrices, 198–200

Human Genome Project, 6

hypercomplex number, 194–195, 208–209

indel (insertion/deletion), 68–69, 71, 73–74

informatics, 18, 249–251, 253, 255–256, 258

298 INDEX

Jones polynomial, 101

Julia fractals, 159–160

knot polynomial, 89, 101

knot theory, 14, 89, 101–102, 105

Laurent polynomial, 101

linking number, 89, 95–98, 102–104, 106, 111

local alignment, 69, 72–75, 82, 84, 87

Basic Local Alignment Sequence Tool

(BLAST), 72

optimal local alignment, 72–73

Mandelbrot set, 159–160

Markov model, 82–83

regular and hidden Markov models, 83

matrix genetics, 181, 190, 213–214, 218, 224,

226–227

Modulo-2 addition, 38–39, 53

Morptology, 1

multiple sequence alignment, 63, 67, 75–76,

78–80, 85, 87

proﬁ le analysis, 78

nearest-neighbor search, 115

neuroscience, 229, 237, 240–243

noise-immunity, 24, 30, 91

coding 25, 29, 34, 199, 225, 227

nucleosome, 90–91, 105–107

formation, 90

core, 91

winding in nucleosomes, 106

pairwise sequence alignment, 63, 67, 69

primary structure, 112–113, 118–119, 125, 130

polygon, 114–115

Voronoi polygons, 115

partitioning, 115

polymerase, 5,

DNA polymerase,

RNA polymerase,

polymerase chain reaction (PCR), 5

thermostable polymerase

quaternary structure, 112–113, 117–120

quantum computer, 180–181, 195, 197, 226

quaternions, 202, 204, 207, 209, 223

by Hamilton, 204, 207

purine quaternions, 209

genoquaternions, 209, 223

Rademacher functions, 16, 181, 183,

185–188, 190, 195, 208, 224–225

random network, 142, 146

Bernoulli random network, 142

reading frame, 67

regular graph, 139, 146

Reidemeister move, 94–95, 97, 99

of the type I, 94–96

of the types II and III, 94–95

replication, 254–255, 258

scale-free network, 143, 147

network paradigms, 146

secondary structure, 112–113, 118–122,

125

secondary structure prediction, 121,

125

self-similarity, 159, 162, 172

Sierpinski triangle, 160–162

supercoil (supercoiling), 90–92, 99,

102–107, 109–111

negative and positive supercoils, 91

plectonemic supercoiling, 99

the density of supercoiling, 104

superhelicity, 91, 103

tangle, 89, 98–101, 106–107, 111

rational tangles, 99–111

tetra-reproduction, 188

tertiary structure, 112–113, 118, 120, 125,

130, 132, 134

tertiary structure prediction, 113, 125

topology, 13, 113–114, 116, 132

transcription, 253–255, 258

transcription unit, 255

translation, 253–255, 258

transposons, 3

U-algorithm, 194, 197–200, 212, 214

universal evolution, 252

Walsh functions, 6, 17, 22, 181, 190, 194–195,

197, 224–226

x-ray diffraction, 3

Wiley Series on

Bioinformatics: Computational Techniques and Engineering

Bioinformatics and computational biology involve the comprehensive application of

mathematics, statistics, science, and computer science to the understanding of living systems.

Research and development in these areas require cooperation among specialists from the ﬁ elds

of biology, computer science, mathematics, statistics, physics, and related sciences. The objective

of this book series is to provide timely treatments of the different aspects of bioinformatics

spanning theory, new and established techniques, technologies and tools, and application

domains. This series emphasizes algorithmic, mathematical, statistical, and computational

methods that are central in bioinformatics and computational biology.

Series Editors: Professor Yi Pan and Professor Albert Y. Zomaya

pan@cs.gsu.edu zomaya@it.usyd.edu.au

Knowledge Discovery in Bioinformatics: Techniques, Methods, and Applications

Xiaohua Hu and Yi Pan

Grid Computing for Bioinformatics and Computational Biology

Edited by El - Ghazali Talbi and Albert Y. Zomaya

Bioinformatics Algorithms: Techniques and Applications

Ion Mandiou and Alexander Zelikovsky

Analysis of Biological Networks

Edited by Bj ö rn H. Junker and Falk Schreiber

Computational Intelligence and Pattern Analysis in Biological Informatics

Edited by Ujjwal Maulik, Sanghamitra Bandyopadhyay, and

Jason T. L. Wang

Mathematics of Bioinformatics: Theory, Practice, and Applications

Matthew He and Sergey Petoukhov