Index

BLAST

DNA-DNA hybridisation

GO

ORF

PCR

--> reverse transcription

allele

--> diploid

--> locus

basal

bilateria

chromatin

cleavage

coelom

--> bilateria

diploid

gene mapping

--> locus

genetic map

--> locus

haplotype

heterozygous

--> diploid

histone

--> chromatin

holoblaste

--> cleavage

homologous

--> orthologous

--> diploid

--> paralogous

homozygous

--> diploid

in-paralogs

--> paralogous

locus

monophyly

--> bilateria

orthologous

out-paralogs

--> paralogous

outgroup

--> basal

paralogous

paraphyly

percent homology

--> homologous

pseudocoelom

--> bilateria

pseudogene

reverse transcription

--> pseudogene

sequence

sequence similarity

--> homologous

stop codon

--> ORF

Definitions

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‣ BLAST:

The name is the acronym of "Basic Local Alignment Search Tool".

A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold. Different types of BLASTs are available according to the query sequences. For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence[1].

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‣ DNA-DNA hybridisation:

Technique used for comparing the degree of genetic similarity between pools of DNA sequences. It is usually used to determine the genetic distance between two species. It is kind of an "analogic" technique greatly superseeded by digital comparison of sequences.

From wikipedia[1]:

It consists on the following: the DNA of one organism is labeled, then mixed with the unlabeled DNA to be compared against. The mixture is incubated to allow DNA strands to dissociate and reanneal, forming hybrid double-stranded DNA. Hybridized sequences with a high degree of similarity will bind more firmly, and require more energy to separate them: i.e. they separate when heated at a higher temperature than dissimilar sequences, a process known as "DNA melting". To assess the melting profile of the hybridized DNA, the double-stranded DNA is bound to a column and the mixture is heated in small steps. At each step, the column is washed; sequences that melt become single-stranded and wash off the column. The temperatures at which labeled DNA comes off the column reflects the amount of similarity between sequences (and the self-hybridization sample serves as a control). These results are combined to determine the degree of genetic similarity between organisms.

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‣ GO:

The acronym for the "Gene Ontology" website: "The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data."[2]

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‣ ORF:

Open Reading Frame.

Here is the example in the Wikipedia article:

If a portion of a genome has been sequenced (e.g. 5'-ATCTAAAATGGGTGCC-3'), ORFs can be located by examining each of the three possible reading frames on each strand. In this sequence two out of three possible reading frames are entirely open, meaning that they do not contain a stop codon,

:

...A TCT AAA ATG GGT GCC...

...AT CTA AAA TGG GTG CC...

...ATC TAA AAT GGG TGC C...

:

Possible stop codons in DNA are "TGA", "TAA" and "TAG". Thus, the last reading frame in this example contains a stop codon (TAA), unlike the first two.

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‣ PCR:

The polymerase chain reaction (PCR) is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.

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‣ allele:

An allele is one of two or more forms of genes (generally a group of genes).[1][2] Sometimes, different alleles can result in different traits, such as pigmentation. At other times, different alleles give rise to the same trait, since some variations at the genetic level result in little or no variation of a trait.

Most multicellular organisms have two sets of chromosomes, that is, they are diploid. These chromosomes are referred to as homologous chromosomes. Diploid organisms have one copy of each gene (and therefore one allele) on each chromosome. If both alleles are the same, they are homozygotes. If the alleles are different, they are heterozygotes.

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‣ basal:

In phylogenetics, a basal clade is the earliest clade to branch in a larger clade; it appears at the base of a cladogram.

A basal group forms an outgroup to the rest of the clade.

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‣ bilateria:

A monophyletic group. From wikipedia[1]:

For the most part, they are bilaterally symmetric, and often have a specialized head with feeding and sensory organs. The body is triploblastic, i.e. all three germ layers are well-developed, and tissues form distinct organs. The digestive chamber has two openings, a mouth and an anus, and there is also an internal body cavity called a coelom or pseudocoelom. There are exceptions to each of these characteristics, however -- for instance adult echinoderms are radially symmetric, and certain parasitic worms have extremely simplified body structures.

------------------------------

‣ chromatin:

Chromatin is the combination of DNA and proteins that make up the contents of the nucleus of a cell. The primary functions of chromatin are to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, and to control gene expression and DNA replication. The primary protein components of chromatin are histones that compact the DNA. Chromatin is only found in eukaryotic cells: prokaryotic cells have a very different organization of their DNA which is referred to as genophore (not chromatin).

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‣ cleavage:

In embriology, it is the division of cells in the early embryo. There are several kinds of cleavage; mammal use the so called "rotational", which is a subtype of "holoblastic" cleavage.

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‣ diploid:

Diploid (indicated by 2n = 2x) cells have two homologous copies of each chromosome, usually one from the mother and one from the father. Nearly all mammals are diploid organisms (the tetraploid viscacha rats Pipanacoctomys aureus and Tympanoctomys barrerae are the only known exceptions as of 2004), although all individuals have some small fraction of cells that display polyploidy. Human diploid cells have 46 chromosomes and human haploid gametes (egg and sperm) have 23 chromosomes.

Retroviruses that contain two copies of their RNA genome in each viral particle are also said to be diploid. Examples include human foamy virus, human T-lymphotropic virus, and HIV

Diploid and polyploid cells whose chromosomes have the same allele of a given gene at some locus are called homozygous with respect to that gene, while those that have different alleles of a given gene at a locus, heterozygous with respect to that gene.

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‣ haplotype:

?

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‣ histone:

In biology, histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and play a role in gene regulation. Without histones, the unwound DNA in chromosomes would be very long (a length to width ratio of more than 10 million to one in human DNA). For example, each human cell has about 1.8 meters of DNA, but wound on the histones it has about 90 micrometers (0.09 mm) of chromatin, which, when duplicated and condensed during mitosis, result in about 120 micrometers of chromosomes.

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‣ homologous:

Used more in the sense of sequence homology. Citing Wikipedia, homology between protein or DNA sequences is defined in terms of shared ancestry.

Note this: "homology among proteins or DNA is often incorrectly concluded in the bases of sequence similarity". Sequence similarity might occur because of evolution convergence. In those cases, the terms "percent homology" and "sequence similarity" are used.

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‣ locus:

In the fields of genetics and genetic computation, a locus (plural loci) is the specific location of a gene or DNA sequence on a chromosome. A variant of the DNA sequence at a given locus is called an allele. The ordered list of loci known for a particular genome is called a genetic map. Gene mapping is the process of determining the locus for a particular biological trait.

The chromosomal locus of a gene might be written "6p21.3", where 6 is the chromosome number, p indicates the chromosome's short arm (q would indicate the long arm).

The numbers that follow the letter represent the position on the arm: band 2, section 1, sub-band 3. The bands are visible under a microscope when the chromosome is suitably stained. Each of the bands is numbered, beginning with 1 for the band nearest the centromere. Sub-bands and sub-sub-bands are visible at higher resolution.

------------------------------

‣ monophyly:

From wikipedia[1]:

In common cladistic usage, a monophyletic group is a taxon (group of organisms) which forms a clade, meaning that it contains all the descendants of the possibly hypothetical closest common ancestor of the members of the group. The term is synonymous with the uncommon term holophyly. Monophyletic groups are typically characterized by shared derived characteristics.

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‣ orthologous:

Homologous sequences are orthologous if they were separated by a speciation event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous.

------------------------------

‣ outgroup:

From wikipedia[1]:

In cladistics or phylogenetics, an outgroup is a (monophyletic) group of organisms that serves as a reference group for determination of the evolutionary relationship among three or more monophyletic groups of organisms.

The chosen outgroup is hypothesized to be rather closely related to the other groups, but less closely than any single one of the other groups is to each other. The evolutionary conclusion from this is that the outgroup branched from the parent group before the other two groups branched from each other.

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‣ paralogous:

Homologous sequences are paralogous if they were separated by a gene duplication event: if a gene in an organism is duplicated to occupy two different positions in the same genome, then the two copies are paralogous. Paralogous genes often belong to the same species, but this is not necessary: for example, the hemoglobin gene of humans and the myoglobin gene of chimpanzees are paralogs. Paralogs can be split into in-paralogs, (paralogous pairs that arose after a speciation event), and out-paralogs (paralogous pairs that arose before a speciation event). Between species out-paralogs are pairs of paralogs that exist between two organisms due to duplication before speciation, whereas within species out-paralogs are pairs of paralogs that exist in the same organism, but whose duplication event happened before speciation. Paralogs typically have the same or similar function, but sometimes do not: due to lack of the original selective pressure upon one copy of the duplicated gene, this copy is free to mutate and acquire new functions.

------------------------------

‣ paraphyly:

From wikipedia[1]:

A group of taxa is said to be paraphyletic if the group consists of all the descendants of a hypothetical closest common ancestor minus one or more monophyletic groups of descendants (typically one such group).

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‣ pseudogene:

This is a contended concept[3].

From Wikipedia: Pseudogenes are dysfunctional relatives of known genes that have lost their protein-coding ability or are otherwise no longer expressed in the cell. Although some do not have introns or promoters (these pseudogenes are copied from mRNA and incorporated into the chromosome and are called processed pseudogenes), most have some gene-like features (such as promoters, CpG islands, and splice sites), they are nonetheless considered nonfunctional, due to their lack of protein-coding ability resulting from various genetic disablements (premature stop codons, frameshifts, or a lack of transcription) or their inability to encode RNA (such as with rRNA pseudogenes)

To some, a pseudogene is a gene-like structure that contains in-frame stop codons or evidence of reverse transcription. To others, the definition of a pseudogene is expanded to include gene structures that contain full open reading frames but are not transcribed[3].

The same source has still more examples.

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‣ reverse transcription:

According to wikipedia, it is a laboratory technique:

Reverse transcription polymerase chain reaction (RT-PCR) is a variant of polymerase chain reaction (PCR), a laboratory technique commonly used in molecular biology to generate many copies of a DNA sequence, a process termed "amplification". In RT-PCR, however, an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional PCR or real-time PCR. Reverse transcription PCR is not to be confused with real-time polymerase chain reaction (Q-PCR/qRT-PCR), which is also sometimes abbreviated as RT-PCR.

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‣ sequence:

It mostly referes to peptide sequences and necleotide sequences. The last, then, is subdivided in RNA and DNA.

Bibliography

[1] en.wikipedia.org

[2] www.geneontology.org

[3] Integrating biological databases. Lincoln D. Stein

Table of Contents

Index

Definitions

Bibliography