He M., Petoukhov S. Mathematics of Bioinformatics: Theory, Methods and Applications

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APPENDIX C: BIOINFORMATICS GLOSSARY 283

Microarray: a two - dimensional array, typically on a glass, ﬁ lter, or silicon

wafer, upon which genes or gene fragments are deposited or synthesized in

a predetermined spatial order, allowing them to be made available as

probes in a high - throughput, parallel manner.

MIM number (also known as MIM# , OMIM number , or McKusick code )

1,2

: a

unique six - digit number assigned to each entry listed in the catalog of

human genes and genetic disorders, “ Online Mendelian Inheritance in

Man ” (OMIM). The ﬁ rst digit of a MIM number describes a gene ’ s mode

of inheritance as outlined below.

First Digit Format

Mode of Inheritance

1 1XXXXX Autosomal dominant (for entries

created before May 15, 1994)

2 2XXXXX Autosomal recessive (for entries

created before May 15, 1994)

3 3XXXXX X - linked loci or phenotypes

4 4XXXXX Y - linked loci or phenotypes

5 5XXXXX Mitochondrial loci or phenotypes

6 6XXXXX Autosomal loci or phenotypes (for

entries created after May 15, 1994)

X is any digit.

Mismatch score: the penalty assigned by an algorithm when nonidentical

restudies are aligned in an alignment.

Missense mutation: a point mutation in which one codon (triplet of bases) is

changed into another, designating a different amino acid.

Mitochondiral signal sequence: a string of amino acids that causes a eukary-

otic protein to be delivered to a cell ’ s mitochondria.

Modeling: ( in bioinformatics ) refers to molecular modeling, a process whereby

the three - dimensional architecture of biological molecules is interpreted

(or predicted), visually represented, and manipulated in order to determine

their molecular properties. ( general ) a series of mathematical equations or

procedures that simulate a real - life process given a set of assumptions,

boundary parameters, and initial conditions.

Monomer: a single unit of any biological molecule or macromolecule, such as

an amino acid, nucleic acid, polypeptide domain, or protein.

Motif: a conserved element of a protein sequence alignment that usually cor-

relates with a particular function. Motifs are generated from a local multiple

protein sequence alignment corresponding to a region whose function or

structure is known. It is sufﬁ cient that it is conserved, and is hence likely to

be predictive of any subsequent occurrence of such a structural or func-

tional region in any other novel protein sequence. A motif is built from

284 APPENDIX C: BIOINFORMATICS GLOSSARY

particular combinations of secondary structures (typically, α - helices and

β - sheets).

Multiple (sequence) alignment: a multiple alignment of k sequences is a rect-

angular array, consisting of characters taken from the alphabet A that satis-

ﬁ es the following conditions: There are exactly k rows; ignoring the gap

character, row i is exactly the sequence sI ; and each column contains at least

one character different from – . In practice, multiple sequence alignments

include a cost/weight function, which deﬁ nes the penalty for the insertion

of gaps (the – character) and weights identities and conservative substitu-

tions accordingly. Multiple alignment algorithms attempt to create the

optimal alignment, deﬁ ned as the one with the lowest cost/weight score.

Multiplex sequencing: an approach to high - throughput sequencing that uses

several pooled DNA samples run through gels simultaneously and then

separated and analyzed.

Mutation: an inheritable alteration to the genome that includes genetic (point

or single base) changes, or larger - scale alterations such as chromosomal

deletions or rearrangements.

Naked DNA: pure, isolated DNA devoid of any proteins that may bind to it.

Native structure (conformation): unique structure into which a particular

protein is usually folded within a living cell.

Nested PCR: the second round ampliﬁ cation of an already PCR - ampliﬁ ed

sequence using a new pair of primers which are internal to the original

primers, typically done when a single PCR reaction generates insufﬁ cient

amounts of product.

Neural net: an interconnected assembly of simple processing elements, units,

or nodes whose functionality is based loosely on the animal brain. The

processing ability of the network is stored in the interunit connection

strengths, or weights, obtained by a process of adaptation to, or learning

from, a set of training patterns. Neural nets are used in bioinformatics to

map data and make predictions, such as taking a multiple alignment of a

protein family as a training set in order to identify novel members of the

family from their sequence data alone.

Neutral mutation: a mutation that has no effect on the ﬁ tness of an

organism.

NMR (nuclear magnetic resonance): a technique for resolving protein

structures.

Nonhomologous chromosomes: chromosomes that are not of the same size

and shape and contain different genes. For example, a typical human being

has 23 different types of nonhomologous chromosomes.

Nonsense mutation: a point mutation in which a codon speciﬁ c for an amino

acid is converted into a stop codon.

Nuclease: any enzyme that can cleave the phosphodiester bonds of nucleic

acid backbones.

APPENDIX C: BIOINFORMATICS GLOSSARY 285

Nucleoside: a ﬁ ve - carbon sugar covalently attached to a nitrogen base (a

nucleotide without the phosphate group added).

Nucleotide: a nucleic acid unit composed of a ﬁ ve - carbon sugar joined to a

phosphate group and a nitrogen base.

Object - relational database: databases that combine the elements of object

orientation and object - oriented programming languages with database

capabilities. They provide more than persistent storage of programming

language objects. Object databases extend the functionality of object pro-

gramming languages (e.g., C + + , Smalltalk, Java) to provide full - featured

database programming capability. The result is a high level of congruence

between the data model for the application and the data model of the

database. Object - relational databases are used in bioinformatics to map

molecular biological objects (such as sequences, structures, maps, and path-

ways) to their underlying representations (typically, within the rows and

columns of relational database tables). This enables users to deal with the

biological objects in a more intuitive manner, as they would in the labora-

tory, without having to worry about the underlying data model of their

representation.

Oligonucleotide: a short molecule consisting of several linked nucleotides

(typically, between 10 and 60) attached covalently by phosphodiester bonds.

Open reading frame (ORF): any stretch of DNA that potentially encodes a

protein. Open reading frames start with an initiation (or start) codon and

end with a termination (or stop) codon. No termination codons may be

present internally. The identiﬁ cation of an ORF is the ﬁ rst indication that

a segment of DNA may be part of a functional gene.

Operator: a segment of DNA that interacts with the products of regulatory

genes and facilitates the transcription of one or more structural genes.

Operon: in prokaryotes, a unit of transcription consisting of one or more

structural genes, an operator, and a promoter.

Orthologs: genes in different species that evolved from a common ancestral

gene by speciation. Normally, orthologs retain the same function in the

course of evolution. Identiﬁ cation of orthologs is critical for reliable predic-

tion of gene function in newly sequenced genomes.

Orthologous genes

1,2

: homologous sequences in different species that result

from a common ancestral gene during speciation. Orthologous genes may

or may not have similar functions.

Overlapping clones: a collection of cloned sequences made by generating

randomly overlapping DNA fragments with infrequently cutting restriction

enzymes.

Palindrome: a region of DNA with a symmetrical arrangement of bases occur-

ring about a single point such that the base sequences on either side of that

point are identical (if the strands are both read in the same direction; e.g.,

5 ′ - GAATTC - 3 ′ , whose complementary sequence is 3 ′ - CTTAAG - 5 ′ ).

286 APPENDIX C: BIOINFORMATICS GLOSSARY

Paralogous genes

1,2

: homologous sequences within a single species that are

the result of gene duplication.

Parameters: user - selectable values, typically determined experimentally, that

govern the boundaries of an algorithm or program. For example, selection

of the appropriate input parameters governs the success of a search algo-

rithm. Some of the most common search parameters in bioinformatics tools

include the stringency of an alignment search tool and the weights (penal-

ties) provided for mismatches and gaps.

Pathways: bioinformatics strives to deﬁ ne representations of key biological

datatypes, algorithms, and inference procedures, including sequences, struc-

tures, biological pathways, and reactions. Representing and computing with

biological pathways requires ontologies for representing pathway knowl-

edge, user interfaces to these databases, physicochemical properties of

enzymes and their substrates in pathways, and pathway analysis of whole

genomes, including identifying common patterns across species and species

differences.

Pattern: a molecular biological pattern usually occurs at the level of the char-

acters making up a gene or protein sequence. A pattern language must be

deﬁ ned in order to apply different criteria to different positions of a

sequence. In enable a computer to carry out position - speciﬁ c comparisons,

a pattern - matching algorithm must allow alternative residues at a given

position, repetitions of a residue, exclusion of alternative residues, weight-

ing, and ideally, combinatorial representation.

Peptide: a short stretch of amino acids each covalently coupled by a peptide

(amide) bond.

Peptide bond (amide bond): a covalent bond formed between two amino

acids when the amino group of one is linked to the carboxy group of

another (resulting in the elimination of one water molecule).

pH: a unit of measure used to indicate the concentration of hydrogen ions in

a solution; speciﬁ cally, the negative log of the molar concentration of H

The greater the concentration of H

, the lower the pH.

Phenotype: any observable feature of an organism that is the result of one or

more genes.

Physical map: a linearly ordered set of DNA fragments encompassing the

genome or region of interest. Physical maps are of two types. A macror-

estriction map consists of an ordered set of large DNA fragments generated

using restriction enzymes whose recognition sequences are represented

infrequently in the genome. An ordered clone map consists of an overlap-

ping collection of cloned DNA fragments.

Plasmid: any replicating DNA element that can exist in the cell independent

of the chromosomes. Synthetic plasmids are used for DNA cloning. Most

commonly found naturally in bacterial cells as a ring of DNA.

APPENDIX C: BIOINFORMATICS GLOSSARY 287

Point mutation: a mutation in which a single nucleotide in a DNA sequence

is substituted for another nucleotide.

Poly(A) tail: the stretch of adenine (A) residues at the 3 ′ end of eukaryotic

mRNA that is added to the pre - mRNA as it is processed, before its trans-

port from the nucleus to the cytoplasm and subsequent translation at the

ribosome.

Polyadenylation site: a site on the 3 ′ end of messenger RNA (mRNA) that

signals the addition of a series of adenines during the RNA processing step

and before the mRNA migrates to the cytoplasm. These poly(A) “ tails ”

increase mRNA stability and allow one to isolate mRNA from cells by

reverse transcriptase PCR ampliﬁ cation using poly(T) primers.

Polygenic inheritance: inheritance involving alleles at many genetic loci.

Polymerase chain reaction (PCR): a technique used to amplify or generate

large amounts of replicated DNA of a segment of any DNA whose “ ﬂ ank-

ing ” sequences are known.

Polymorphism: the existence of a gene in a population in at least two different

forms at a frequency far higher than that attributable to recurrent mutation

alone. Variations in a population may be measured by determining the rate

of mutation in polymorphic genes.

Polypeptide (chain)

1,2

: a single chain of covalently attached amino acids joined

by peptide bonds. A polypeptide chain usually consists of 100 or fewer

amino acids. Polypeptide chains usually fold into a compact, stable form (a

domain) that is part (or all) of the ﬁ nal protein. A protein is made up of

one or several polypeptide chains.

Primary structure

1,2

: the amino acid sequence of a polypeptide chain. Of the

four levels of protein structure, this is the most basic protein structure.

Primer: a short oligonucleotide that provides a free 3 ′ hydroxyl for DNA or

RNA synthesis by the appropriate polymerase (DNA polymerase or RNA

polymerase).

Probe: any biochemical that is labeled or tagged in some way so that it can

be used to identify or isolate a gene, RNA, or protein.

Proﬁ le: a sequence proﬁ le is usually derived from multiple alignments of

sequences with a known relationship, and consists of a table of position -

speciﬁ c scores and gap penalties. Each position in a proﬁ le contains scores

for all possible amino acids, as well as one penalty score for opening and

one for continuing a gap at the position speciﬁ ed. Attempts have been made

to further improve the sensitivity of a proﬁ le by reﬁ ning the procedures to

construct the proﬁ le, starting from a given multiple alignment. Other rep-

resentations for sequence domains or motifs do not necessarily require the

presence of a correct and complete multiple alignment, such as hidden

Markov models.

288 APPENDIX C: BIOINFORMATICS GLOSSARY

Prokaryote: an organism or cell that lacks a membrane - bound nucleus.

Bacteria and blue - green algae are the only surviving prokaryotes. ( See also

Eukaryote.)

Promoter site: d e ﬁ ned by its recognition of eukaryotic RNA polymerase II;

its activity in a higher eukaryote; by experimental evidence, or homology

and sufﬁ cient similarity to an experimentally deﬁ ned promoter; and by

observed biological function.

Protein families: sets of proteins that share a common evolutionary origin

reﬂ ected by their relatedness in function, which is usually reﬂ ected by simi-

larities in sequence or in primary, secondary, or tertiary structure. Families

are subsets of proteins with related structure and function.

Protein ID (in GenBank)

1,2

: an identiﬁ cation number assigned to the amino

acid sequence data included within a sequence record. This sequence identi-

ﬁ er uses the accession.version format. Each protein ID is made up of three

letters, followed by ﬁ ve digits, a period, and a version number. For example,

in sequence record M12345, the Protein ID for the sequence translation

could be AAA35650.1. If the protein sequence data change in any way

(even by only one amino acid), the version number in the Protein ID will

be increased by an increment of one while the accession number base

remains constant; for example, AAA12345.1 would become AAA12345.2.

Each amino acid sequence change also results in the assignment of a new

GI number to the altered protein translation.

Proteome: the entire protein complement of a given organism.

Proteomics: the study of a proteome. Typically, the cataloging of all the express-

ed proteins in a particular cell or tissue type, obtained by identifying the

proteins from cell extracts using a combination of two - dimensional gel elec-

trophoresis and mass spectrometry. Proteomics includes the large - scale anal-

ysis of the amassed protein composition and function. ( See also Genomics.)

Purine: a nitrogen - containing compound with a double - ring structure. The

parent compound of adenine and guanine.

Pyrimidine: a nitrogen - containing compound with a single six - membered

ring structure. The parent compound of thymidine (uracil in RNA) and

cytosine.

Quaternary structure

1,2

: the interconnection and arrangement of polypeptide

chains within a protein. Only proteins with more than one polypeptide

chain can have quaternary structure.

Query (sequence): a DNA, RNA of protein sequence used to search a

sequence database in order to identify close or remote family members

(homologs) of known function, or sequences with similar active sites or

regions (analogs), from whom the function of the query may be deduced.

Reading frame: a sequence of codons beginning with an intiation (or start)

codon and ending with a termination (or stop) codon, typically of at least

150 bases (50 amino acids), coding for a polypeptide or protein chain.

APPENDIX C: BIOINFORMATICS GLOSSARY 289

Recombinant DNA (rDNA): DNA molecules resulting from the fusion of

DNA from different sources. The technology employed for splicing DNA

from different sources and for amplifying the resulting heterogeneous

DNA.

Recombination: a new combination of alleles resulting from the rearrange-

ment occuring by crossing over or by independent assortment. ( See also

Crossing over.)

Recursion: an algorithmic procedure whereby an algorithm calls on itself to

perform a calculation until the result exceeds a threshold, in which case the

algorithm exits. Recursion is a powerful procedure with which to process

data and is computationally quite efﬁ cient.

Regulatory gene: a DNA sequence that functions to control the expression

of other genes by producing a protein that modulates the synthesis of their

products (typically by binding to the gene promoter). ( See also Structural

gene.)

Relational database: a database that follows E. F. Codd ’ s 11 rules, a series of

mathematical and logical steps for the organization and systemization of

data into a software system that allows easy retrieval, updating, and

expansion.

Relational database management systems (RDBMS): a software system that

includes a database architecture, query language, and data loading and

updating tools and other ancillary software that together allow the creation

of a relational database application. An RDBMS stores data in a database

consisting of one or more tables of rows and columns. The rows correspond

to a record (tuple); the columns correspond to attributes (ﬁ elds) in the

record. In an RDBMS, a view, deﬁ ned as a subset of the database that is

the result of the evaluation of a query, is a table. RDBMSs use Structured

Query Language (SQL) for data deﬁ nition, data management, and data

access and retrieval. Relational and object - relational databases are used

extensively in bioinformatics to store sequences and other biological data.

Repeats (repeat sequences): repeat sequences and approximate repeats occur

throughout the DNA of higher organisms (mammals). For example, Alu

sequences of about 300 characters in length appear hundreds of thousands

of times in human DNA, with about 87% homology to a consensus Alu

string. Some short substrings, such as TATA - boxes, poly - A, and (TG) * , also

appear more often than would be expected by chance. Repeat sequences

may also occur within genes, as mutations or alterations to those genes.

Repetitive sequences, especially mobile elements, have many applications

in genetic research. DNA transposons and retroposons are used routinely

for insertional mutagenesis, gene mapping, gene tagging, and gene transfer

in several model systems.

Repetitive elements: elements that provide important clues about chromo-

some dynamics, evolutionary forces, and mechanisms for exchange of

genetic information between organisms. The most ubiquitous class of

290 APPENDIX C: BIOINFORMATICS GLOSSARY

repetitive elements in the DNA sequence in primate genomes is the Alu

family of interspersed repeats, which have arisen in the last 65 million years

of evolution. Alu repeats belong to a class of sequences deﬁ ned as short

interspersed elements (SINEs). Approximately 500,000 Alu SINEs exist

within the human genome, representing about 5% of the genome by mass.

The pattern of these repeats in the human population can be used to

address questions of large - scale genealogy.

Replication: the synthesis of an informationally identical macromolecule (e.g.,

DNA) from a template molecule.

Repressor: the protein product of a regulatory gene that combines with a

speciﬁ c operator (regulatory DNA sequence) and hence blocks the tran-

scription of genes in an operon.

Residue: the portion of an amino acid that remains a part of a polypeptide

chain. In the context of a peptide or protein, amino acids are generally

referred to as residues.

Restriction enzyme (restriction endonuclease): a type of enzyme that recog-

nizes speciﬁ c DNA sequences (usually, palindromic sequences 4, 6, 8, or 16

base pairs in length) and produces cuts on both strands of DNA containing

those sequences only.

Restriction map: a physical map or depiction of a gene (or genome) derived

by ordering overlapping restriction fragments produced by digestion of the

DNA with a number of restriction enzymes.

Retroposons: mobile DNA segments that insert into chromosomes after they

have been reverse - transcribed from an RNA molecule.

Reverse genetics: the use of protein information to elucidate the genetic

sequence encoding that protein.

Reverse transcriptase: a DNA polymerase that can synthesize a complemen-

tary DNA (cDNA) strand using RNA as a template; called RNA - dependent

DNA polymerase.

Ribosomal RNA (rRNA): a type of rRNA that plays a large structural role

in determining the structure and function of the ribosome (cellular struc-

ture on which proteins are assembled).

RNA (ribonucleic acid): a category of nucleic acids in which the component

sugar is ribose and consisting of the four nucleotides: thymidine, uracil,

guanine, and adenine. The three types of RNA are messenger RNA (mRNA),

transfer RNA (tRNA), and ribosomal RNA (rRNA).

Secondary structure

1,2

: the folded, coiled, or twisted shape of a polypeptide

that results from hydrogen bonding between parts of a molecule. There are

two main types of secondary structure: an α - helix and a β - pleated sheet.

Selectivity: the selectivity of bioinformatics similarity search algorithms is

deﬁ ned as the signiﬁ cance threshold for reporting database sequence

matches. For example, in BLAST searches, the parameter E is interpreted

as the upper bound on the expected frequency of chance occurrence of a

APPENDIX C: BIOINFORMATICS GLOSSARY 291

match within the context of the entire database search. E may be thought

of as the number of matches that one expects to observe by chance alone

during a database search.

Sensitivity: the sensitivity of bioinformatics similarity search algorithms

centers around two areas: how well the method can detect biologically

meaningful relationships between two related sequences in the presence of

mutations and sequencing errors; and how the heuristic nature of the algo-

rithm affects the probability that a matching sequence will not be detected.

At the user ’ s discretion, the speed of most similarity search programs can

be sacriﬁ ced in exchange for greater sensitivity — with an emphasis on

detecting lower - scoring matches.

Sequence tagged site (STS)

1,2

: a short (200 to 500 base pairs) DNA sequence

that has a single occurrence in the human genome and whose location and

base sequence are known. Detectable by polymerase chain reaction, STSs

are useful for localizing and orienting the mapping and sequence data

reported from many different laboratories and serve as landmarks for

developing physical maps of the human genome. Expressed sequence tags

(ESTs) are STSs derived from cDNAs.

Shotgun cloning: the cloning of an entire gene segment or genome by generat-

ing a random set of fragments using restriction endonucleases to create a

gene library that can subsequently be mapped and sequenced to reconstruct

the entire genome.

Signal sequence (leader sequence): a short sequence added to the amino -

terminal end of a polypeptide chain that forms an amphipathic helix allow-

ing the nascent polypeptide to migrate through membranes such as the

endoplasmic reticulum or the cell membrane. It is cleaved from the poly-

peptide after the protein has crossed the membrane.

Similarity (homology) search: given a newly sequenced gene, there are two

main approaches to the prediction of structure and function from the amino

acid sequence. Homology methods are the most powerful and are based on

the detection of signiﬁ cant extended sequence similarity to a protein of

known structure, or of a sequence pattern characteristic of a protein family.

Statistical methods are less successful but more general and are based on

the derivation of structural preference values for single residues, pairs

of residues, short oligopeptides, or short sequence patterns. The transfer of

structure and function information to a potentially homologous protein

is straightforward when the sequence similarity is high and extended in

length, but the assessment of the structural signiﬁ cance of sequence similar-

ity can be difﬁ cult when sequence similarity is weak or restricted to a short

region.

Single nucleotide polymorphisms (SNPs): variations of single base pairs scat-

tered throughout the human genome that serve as measures of genetic

diversity in humans. About 1 million SNPs are estimated to be present in

the human genome, and SNPs are useful markers for gene mapping studies.

292 APPENDIX C: BIOINFORMATICS GLOSSARY

Single - pass sequencing: rapid sequencing of large segments of the genome of

an organism by isolating as many expressed (cDNA) sequences as possible

and performing single sequencer runs on their 5 ′ or 3 ′ ends. Single - pass

sequencing typically results in individual, error - prone sequencing reads of

400 to 700 bases, depending on the type of sequencer used. However, if

many of these are generated from numerous clones from different tissues,

they may be overlapped and assembled to remove the errors and generate

a contiguous sequence for the entire expressed gene.

Site(s): sites in sequences can be located either in DNA (e.g., binding sites,

cleavage sites) or in proteins. To identify a site in DNA, ambiguity symbols

are used to allow several different symbols at one position. Proteins need

a different mechanism, however ( see Pattern). Restriction enzyme cleavage

sites, for example, have the following properties: limited length (typically,

fewer than 20 base pairs); deﬁ nition of the cleavage site and its appearance

(3 ′ , 5 ′ overhang or blunt); deﬁ nition of the binding site.

Splicing: the joining together of separate DNA or RNA component parts. For

example, RNA splicing in eukaryotes involves the removal of introns and

the stitching together of the exons from the pre - mRNA transcript before

maturation.

Start codon: a triplet codon (i.e., AUG) at which both prokaryotic and eukary-

otic ribosomes begin to translate the mRNA.

Stop codon: one of three triplet codons (UGA, UAG, and UAA) that does

not instruct the ribosome to insert a speciﬁ c amino acid and thereby causes

translation of an mRNA to stop. Instead, a termination factor is typically

inserted, causing the ribosome to be disassembled and the completed

protein to be released.

Structural gene: a gene that encodes a structural protein.

Structure prediction: algorithms that predict the secondary, tertiary, and

sometimes even quarternary structure of proteins from their sequences.

Determining protein structure from a sequence has been dubbed “ the

second half of the genetic code ” since it is the higher - level folded structure

of a protein that governs how it functions as a gene product. As yet, most

structure prediction methods have been only partially successful and typi-

cally work best for certain well - deﬁ ned classes of proteins.

Substitution matrix: a model of protein evolution at the sequence level, result-

ing in the development of a set of widely used substitution matrices. These

are frequently called Dayhoff, MDM (mutation data matrix), BLOSUM, or

PAM (percent accepted mutation) matrices. They are derived from global

alignments of closely related sequences. Matrices for greater evolutionary

distances are extrapolated from those for lesser distances.

Substrate: a specialized type of ligand that binds speciﬁ cally to an enzyme.

Tertiary structure: folding of a protein chain via interactions of its side -

chain molecules, including formation of disulﬁ de bonds between cysteine

residues.