Pathways Project: Reference Glossary

The 3' (three prime) end of a DNA molecule is where the sugar’s third carbon is unattached to an adjacent nucleotide. Since DNA is synthesized in the 5'-to-3' direction, nucleotides are added to the 3' end of the growing strand (cf. 5').

Just like letters and words in the English language are read from left to right, DNA is 'read' in a specific direction 5'-to-3'. The 5' (five prime) end of a DNA molecule is where the sugar’s fifth carbon phosphate group is unattached to an adjacent nucleotide (cf. 3').

In computing, ab initio is a term used to define computations based solely on theory or using only fundamental constants. In computational biology the term refers to algorithms that use only sequence information rather than including experimental observations to make predictions about gene structure.

A unique identification number given to every DNA, RNA, and protein sequence submitted to the National Center for Biotechnology Information (NCBI) or equivalent databases. For example, the accession number for Rheb in D. yakuba is NC_052530 in the NCBI database.

Adenine (A) is one of the four nucleotide bases in DNA, with the other three being cytosine (C), guanine (G) and thymine (T). Within a double-stranded DNA molecule, adenine bases on one strand pair with thymine bases on the opposite strand. The sequence of the four nucleotide bases encodes DNA’s information ^[1].

In bioinformatics, a sequence alignment is a way of arranging two or more sequences of DNA, RNA, or protein to identify regions of similarity; such similarity may be a consequence of functional, structural, or evolutionary relationships between the sequences.

An alignment score is a numerical value used in computational biology to quantify the level of similarity between two aligned sequences. Generally, the higher the score, the more similar the two sequences.

One of the variant forms of a gene at a particular locus on a chromosome. Different alleles produce variation in inherited characteristics such as hair color or blood type. In an individual, one form of the allele (the dominant one) may be expressed more than another form (the recessive one). When “genes” are considered simply as segments of a nucleotide sequence, allele refers to each of the possible alternative nucleotides at a specific position in the sequence. For example, a CT polymorphism such as CCT[C/T]CCAT would have two alleles: C and T ^[2].

The proportion of a specific gene variant (i.e., an allele) among all copies of the gene in the population ^[2].

The inclusion or exclusion of certain exons in the splicing reactions that determine the sequences included in the final mRNA product of a gene. This mechanism is utilized to generate a series of closely related protein isoforms, which differ by the inclusion or exclusion of the protein domains encoded by those exons. Alternative splicing is directed by RNA-binding proteins that block or stimulate utilization of a particular splice site.

Basic building block molecules of peptides and proteins. The sequence of amino acids in a protein is determined by the gene’s codon sequence ^[2].

The basic building block of proteins. There are 20 different amino acids. A protein consists of one or more chains of amino acids (called polypeptides) whose sequence is encoded in a gene ^[1].

Gene annotation is the process of indicating the location, structure, and identity of genes in a genome. As this may be based on incomplete information, gene annotations are constantly changing with improved knowledge. Gene annotation databases change regularly, and different databases may refer to the same gene/protein by different names, reflecting a changing understanding of protein function.

Gene Annotation assigns information to A’s, T’s, G’s, and C’s in DNA sequences; annotations can be divided into two types ^[3]:

The Annotation Files Merger is designed to help you combine the individual files generated by the Gene Model Checker into a single project file suitable for project submission. This tool also performs additional checks to verify that all the isoforms have been annotated and it allows you to view all the annotated gene models on the GEP UCSC Genome Browser. You will only need to merge the files if you have more than one unique isoform. See Part 7.3 of the Pathways Project: Annotation Walkthrough for directions on using the Annotation Files Merger.

The genome assembly is the genome sequence produced after chromosomes have been fragmented, those fragments have been sequenced, and the resulting sequences have been put back together. A genome assembly is updated when DNA has been sequenced that allows gaps to be filled. It may also be updated when a new assembling algorithm is released and applied to the data, resulting in an assembly that’s different from the previous version.

Augustus is an ab initio single isoform gene finder.

Often used as a synonym for adenine (A), cytosine (C), guanine (G) or thymine (T) in DNA.

A base pair consists of two complementary DNA nucleotide bases that pair together to form a "rung of the DNA ladder." DNA is made of two linked strands that wind around each other to resemble a twisted ladder — a shape known as a double helix. Each strand has a backbone made of alternating sugar (deoxyribose) and phosphate groups. Attached to each sugar is one of four bases: adenine (A), cytosine (C), guanine (G) or thymine (T). The two strands are held together by hydrogen bonds between pairs of bases: adenine pairs with thymine (A-T), and cytosine pairs with guanine (C-G) ^[1].

Bioinformatics, as related to genetics and genomics, is a scientific interdisciplinary field that involves using computer technology to collect, store, analyze, and disseminate biological data and information, such as DNA and amino acid sequences or annotations about those sequences. Scientists and clinicians use databases that organize and index such biological information to increase our understanding of health and disease and, in certain cases, as part of medical care ^[1]. At a minimum, it encompasses computer science, biology, genetics, genomics, statistics, mathematics, and engineering to interpret biological data. It is closely related to computational biology ^[2].

BLAST version in which two sequences can be compared to each other. The sequences could either be nucleic acid or protein; select "Align two or more sequences" within a particular BLAST search to use this feature.

Basic Local Alignment Search Tool is a sequence comparison algorithm that is used to search sequence databases for optimal local alignments to a query ^[2]. BLAST finds regions of local similarity between nucleotide or protein sequences by comparing nucleotide or protein sequences to sequence databases (or to an individual nucleotide or protein sequence) and calculates the statistical significance of each match.

BLAST version in which the query and subject are both nucleotide sequences. Typically used to search a nucleotide database with a nucleotide sequence.

BLAST version in which both the query and subject are amino acid sequences. Typically used to search a protein database with a protein sequence.

BLAST version in which the query is nucleotide sequence, and all 6 reading frames are translated and compared to the subject which is an amino acid sequence. Typically used to search a protein database with a nucleotide sequence.

In agreement with existing principles and standards generated from data and evidence. For example, the canonical splice donor sequence is GT. In rare instances, the sequence GC is used instead and since GC is not the "standard," it would be referred to as non-canonical.

A DNA sequence obtained by reverse transcription of a messenger RNA (mRNA) sequence ^[2].

cDNA (short for copy DNA; also called complementary DNA) is synthetic DNA that has been transcribed from a specific mRNA through a reaction using the enzyme reverse transcriptase. While DNA is composed of both coding and non-coding sequences, cDNA contains only coding sequences. Scientists often synthesize and use cDNA as a tool in gene cloning and other research experiments ^[1].

A chromosome is a molecule of double-stranded DNA, carrying an arrangement of genes interspersed with other sequences (e.g., regulatory elements). Chromosomes in eukaryotes are typically linear and extend from one end (a telomere) through the chromosome center (centromere) to the other telomere end.

The portion of the DNA sequence of a gene which is translated into protein. Successful translation of a CDS results in the synthesis of a protein ^[2]. CDS and coding exon are often used interchangeably.

In a gene, any exon which contains some part of the CDS. Coding exon and CDS are often used interchangeably.

The sequence of DNA that is translated into protein and includes an initiation (start) codon and a termination (stop) codon ^[2].

Sequence of three nucleotides in DNA or mRNA that specifies a particular amino acid during protein synthesis; also called a triplet. Of the 64 possible codons, 3 are stop codons, which do not specify amino acids ^[2].

In Euclidean geometry, collinearity refers to a set of points that lie in a straight line. In the context of the tblastn alignments between a protein sequence (query) and a nucleotide sequence (subject), a set of alignments are collinear if the order of the alignment blocks is consistent with the protein sequence. For a protein located on the positive strand of the nucleotide sequence, the subject coordinates for the collinear set of alignment blocks will be in ascending order with respect to the protein sequence. For a protein located on the minus strand of the nucleotide sequence, the subject coordinates for the collinear set of alignment blocks will be in descending order with respect to the protein sequence.

The nucleotide sequence of the nucleic acid strand which would form a double-stranded molecule with the nucleic acid strand in question, using standard base-pairing rules.

When comparing multiple sequences, the consensus sequence reflects the most commonly seen base at each position.

A domain (a distinct functional and/or structural unit of a protein) that has been maintained in the homologous genes of different species during evolution. During evolution, changes at specific positions of an amino acid sequence in the protein may have occurred in a way that preserve the physico-chemical properties of the original amino acid residues, and hence the structural and/or functional properties of that region of the protein ^[2].

Homologous DNA or amino acid sequence with a high degree of similarity between two species.

A contig (as related to genomic studies; derived from the word "contiguous") is a set of DNA segments or sequences that overlap in a way that provides a contiguous representation of a genomic region (cf. scaffold) ^[1].

Numerical position within a biological sequence, e.g., the first base in a DNA sequence would have the coordinate 1.

Cytosine (C) is one of the four nucleotide bases in DNA, with the other three being adenine (A), guanine (G) and thymine (T). Within a double-stranded DNA molecule, cytosine bases on one strand pair with guanine bases on the opposite strand. The sequence of the four nucleotide bases encodes DNA’s information ^[1].

Store of a set of logically related data or collection of files amenable to retrieval using scripts or a computer ^[2].

Data science involves the study of large, complex data sets that arise from various types of research projects. With respect to genomic studies, such work requires expertise in quantitative scientific disciplines such as bioinformatics, computational biology, and biostatistics ^[1].

The removal of some part of a biological sequence.

A deletion, as related to genomics, is a type of mutation that involves the loss of one or more contiguous nucleotides from a segment of DNA. A deletion can involve the loss of any number of nucleotides, from a single nucleotide to an entire piece of a chromosome ^[1].

Analysis of a DNA sequence to predict the location of genes (exons and introns) using only the sequence itself and known characteristics of genes (e.g., consensus splice site sequences in eukaryotic genomes). No knowledge of experimentally confirmed structure or function is used in de novo prediction.

Pattern of gene expression in multi-cellular organisms, where distinct patterns of transcription are shown by different cell types, or at different times during development, or under different environmental conditions.

Deoxyribonucleic acid (abbreviated DNA) is the molecule that carries genetic information for the development and functioning of an organism. DNA is made of two linked strands that wind around each other to resemble a twisted ladder — a shape known as a double helix. Each strand has a backbone made of alternating sugar (deoxyribose) and phosphate groups. Attached to each sugar is one of four bases: adenine (A), cytosine (C), guanine (G) or thymine (T). The two strands are connected by chemical bonds between the bases: adenine bonds with thymine, and cytosine bonds with guanine. The sequence of the bases along DNA’s backbone encodes biological information, such as the instructions for making a protein or RNA molecule ^[1].

DNA sequencing refers to the general laboratory technique for determining the exact sequence of nucleotides, or bases, in a DNA molecule. The sequence of the bases (often referred to by the first letters of their chemical names: A, T, C, and G) encodes the biological information that cells use to develop and operate. Establishing the sequence of DNA is key to understanding the function of genes and other parts of the genome. There are now several different methods available for DNA sequencing, each with its own characteristics, and the development of additional methods represents an active area of genomics research ^[1]. See Sequencing Technologies for more information.

The comparison of two sequences on an X-Y plot where points ("dots") on the graph ("plot") indicate sequence identity at the corresponding positions. A continuous line with slope 1 indicates high levels of sequence conservation in that region and provides confidence in the proposed gene model.

Toward the 3' end of a single stranded DNA molecule or gene of interest (e.g., target gene). Downstream also refers to the genomic region that comes after the feature being examined (cf. upstream).

Duplication, as related to genomics, refers to a type of mutation in which one or more copies of a DNA segment (which can be as small as a few bases or as large as a major chromosomal region) is produced. Duplications occur in all organisms. For example, they are especially prominent in plants, although they can also cause genetic diseases in humans. Duplications have been an important mechanism in the evolution of the genomes of humans and other organisms ^[1] (cf. gene duplication).

The E-value is a parameter that describes the number of hits one can "expect" to see by chance when searching a database of a particular size and complexity. Essentially, the E-value describes the random background noise that exists for matches between sequences. For example, an E-value of 1 assigned to a hit can be interpreted as meaning that in a database of the current size, you might expect to see one match with a similar score simply by chance. This means that the lower the E-value, or the closer it is to "0," the higher is the "significance" of the match. However, it is important to note that searches with short sequences can be virtually identical and have a relatively high E-value. This is because the calculation of the E-value also considers the length of the query sequence and shorter sequences have a high probability of occurring in the database purely by chance ^[2].

Evolution, as related to genomics, refers to the process by which species change over time through changes in the genome. Such evolutionary changes result from mutations that produce genomic variation, giving rise to individuals whose biological functions or physical traits are altered. Those individuals who are best at adapting to their surroundings typically leave behind more offspring than less well-adapted individuals. Thus, over successive generations (in some cases spanning millions of years), one species may evolve to take on divergent functions or physical characteristics or may even evolve into a different species ^[1].

An exon is a region of the genome whose transcription product ends up within a mature mRNA molecule. Some exons are coding, in that they contain information for making a protein, whereas others are non-coding. Genes in the genome consist of exons and introns ^[1]. Although introns are transcribed with the exons, the introns are spliced out and discarded during RNA processing.

ESTs are short (usually approximately 300–500 base pairs), single-pass sequence reads from cDNA. Typically, they are produced in large batches. They represent the genes expressed in a given tissue and/or at a given developmental stage. They are tags (some coding, others not) of expression for a given cDNA library. They are useful in identifying full-length genes and in mapping ^[2].

Any region of defined structure/sequence in a genomic fragment of DNA. Inherent features would include genes, pseudogenes, and repetitive elements. A feature may also be predicted by computational algorithms, such as those aimed at identifying protein-coding genes.

A database of Drosophila genes and genomes

A frame is a single series of adjacent nucleotide triplets in DNA or RNA: one frame would have bases at positions 1, 4, 7, etc. as the first base of sequential codons. There are three possible reading frames in an mRNA strand and six in a double stranded DNA molecule because there are two strands from which transcription is possible. Different computer programs number these frames differently, so care should be taken when comparing designated frames from different programs. One common way is to refer to the three possible left-to-right reading frames as +1, +2, and +3, and the three possible right-to-left reading frames as -1, -2, and -3.

A frameshift mutation in a gene refers to the insertion or deletion of nucleotide bases in numbers that are not multiples of three. This is important because a cell reads a gene’s code in groups of three bases when making a protein. Each of these "triplet codons" corresponds to one of 20 different amino acids used to build a protein. If a mutation disrupts this normal reading frame, then the entire gene sequence following the mutation will be incorrectly read. This can result in the addition of the wrong amino acids to the protein and/or the creation of a codon that stops the protein from growing longer ^[1].

When comparing or aligning two or more protein or nucleic acid sequences, spaces ("gaps") may be introduced in the final alignment to maximize matches and minimize mismatches. Assignment of gaps is dependent on the alignment program and model parameters chosen.

GeMoMa uses conservation of intron positions across different species to improve the accuracy of gene predictions. It also uses sequence similarity to proteins in an informant genome, RNA-Seq read coverage, and splice junction predictions to improve the predictions of protein-coding genes in the target genome.

Basic unit of inheritance; contains the information needed to specify physical and biological traits

Most genes code for specific proteins, or segments of proteins, which have differing functions within the body. Humans have approximately 20,000 protein-coding genes ^[1] and Drosophila melanogaster (fruit flies) have approximately 14,000.

The creation of a second copy of a sequence in a genome. A duplicate copy of a gene may be mutated without affecting the viability of the organism, so gene duplication is thought to be a significant factor in the evolution of genomic diversity (cf. duplication).

Gene expression is the process by which the information encoded in a gene is used to either make RNA molecules that code for proteins or to make non-coding RNA molecules that serve other functions. Gene expression acts as an "on/off switch" to control when and where RNA molecules and proteins are made and as a "volume control" to determine how much of those products are made. The process of gene expression is carefully regulated, changing substantially under different conditions. The RNA and protein products of many genes serve to regulate the expression of other genes ^[1].

Gene mapping refers to the process of determining the location of genes on chromosomes. Today, the most efficient approach for gene mapping involves sequencing a genome and then using computer programs to analyze the sequence to identify the location of genes ^[1].

The description of the exact beginning and ending coordinates within the genome of every exon for a gene and how those exons are assembled into mRNAs; a gene model is the pattern and location of exons, introns, and other elements for an uncharacterized target gene.

A program developed by GEP to test the validity of a proposed gene model after annotation. This program checks that the model complies with easily defined characteristics of a gene including the presence of start and stop codons and proper sequences at intron/exon splice junctions. It does not check for other important characteristics like overlap with evidence for transcription or degree of sequence conservation.

A GEP-developed tool to provide information on Drosophila melanogaster genes, organized to describe how isoforms are related to each other (common and unique exons) and provide protein sequences corresponding to each exon.

Gene regulation is the process used to control the timing, location, and amount in which genes are expressed. The process can be complicated and is carried out by a variety of mechanisms, including through regulatory proteins and chemical modification of DNA. Gene regulation is key to the ability of an organism to respond to environmental changes ^[1].

Genetic code refers to the instructions contained in a gene that tell a cell how to make a specific protein. Each gene’s code uses the four nucleotide bases of DNA: adenine (A), cytosine (C), guanine (G) and thymine (T) — in various ways to spell out three-letter "codons" that specify which amino acid is needed at each position within a protein ^[1].

A genome is all the genetic information an organism carries ^[4]. That is, all the nucleotides, and their order, found in a single cell, or organelle. The entire complement of genetic material of an organism.

The genome is the entire set of DNA instructions found in a cell. A genome contains all the information needed for an individual to develop and function ^[1].

See "assembly"

A local region of the genome containing a small number of genes (5-15) or other features (e.g., repeats). The genomic neighborhood, as related to the Pathways Project, is the region containing the target gene and its neighboring two closest upstream genes and two closest downstream genes.

The genes flanking a particular target gene or other genomic element.

Genomics is a field of biology focused on studying all the DNA of an organism — that is, its genome. Such work includes identifying and characterizing all the genes and functional elements in an organism’s genome as well as how they interact ^[1].

Genomic variation refers to DNA sequence differences among individuals or populations. Some variants influence biological function (such as a mutation that causes a genetic disease), while others have no biological effects ^[1].

Genomics Education Partnership, an awesome (if underappreciated) group of biology educators dedicated to your successfully mastering the fundamentals of genomics!

A genome browser is a web-based visualization tool that allows users to examine the experimental data that provides evidence for a detailed gene structure. The GEP UCSC Genome Browser is a local mirror of the UCSC Genome Browser. It contains the reference sequence and working draft assemblies for many Drosophila genomes currently annotated by students participating in the GEP.

Guanine (G) is one of the four nucleotide bases in DNA, with the other three being adenine (A), cytosine (C) and thymine (T). Within a double-stranded DNA molecule, guanine bases on one strand pair with cytosine bases on the opposite strand. The sequence of the four nucleotide bases encodes DNA’s information ^[1].

A specific member of a group of homologous sequences or molecules; approximately 75% of human disease genes have homologs in Drosophila melanogaster.

In genomics, nucleic acids and proteins are homologous if they evolved from a common ancestor.

Homology is the state of being homologous. Algorithms such as BLAST identify similarity, which is evidence for, but not necessarily proof of, homology. Orthologs and paralogs are subcategories of homology.

A hypothesis is an explanation for an observation which has not been confirmed (or rejected).

Two elements at comparable positions in an alignment (a base or an amino acid) that are the same are said to be identical; the fraction of two sequences which consist of such elements is expressed as "percent identity."

A nonsense mutation changes the codon for an amino acid within an open reading frame into a stop codon. This in-frame stop codon will usually lead to premature termination of translation, which results in a truncated non-functional protein product.

Genome sequences that are aligned to the target species' genome and used as auxiliary information for annotating the target gene. Drosophila melanogaster is the informant species for the Pathways Project annotations.

Type of mutation that involves the addition of DNA within a given sequence; this may occur because of duplication or insertion of foreign sequences such as transposable elements or viral DNA.

Non-coding sections of a eukaryotic nucleic acid sequence found between exons.

An intron is a region that resides within a gene but does not remain in the final mature mRNA molecule following transcription of that gene and does not code for amino acids that make up the protein encoded by that gene ^[1].

An inversion in a chromosome occurs when a segment breaks off and reattaches within the same chromosome, but in reverse orientation. DNA may or may not be lost in the process ^[1].

Potentially different versions of a protein encoded by a single gene. Isoforms result from alternative splicing of a particular pre-mRNA, and/or the use of a different transcription start site.

An alignment where short, highly similar sequences are displayed.

A locus, as related to genomics, is a physical site or location within a genome (such as a gene or another DNA segment of interest), somewhat like a street address ^[1].

Mapping refers to the process of determining the relative locations of landmarks or markers (such as genes (gene mapping), variants, and other DNA sequences of interest) within a chromosome or genome. Historically, there have been two approaches for mapping: physical mapping, which established maps based on physical distances between landmarks, and genetic mapping, which established maps based on the frequency with which two landmarks are inherited together. Today, the most efficient approach for mapping involves sequencing a genome and then using computer programs to analyze the sequence to identify the locations of landmarks ^[1].

Mature messenger RNA that has been completely processed and is ready for translation; it has a 7-methylguanosine cap at its 5' end, a poly-A tail at its 3' end, and has all its introns spliced out.

A mutation is a change in the DNA sequence of an organism. Mutations can result from errors in DNA replication during cell division, exposure to mutagens, or a viral infection. Germline mutations (that occur in eggs and sperm) can be passed on to offspring, while somatic mutations (that occur in body cells) are not passed on ^[1].

National Center for Biotechnology Information

A subset of RefSeq, RefSeqGene defines genomic sequences to be used as reference standards for well-characterized genes. It provides a more stable gene-specific genomic sequence for each gene including upstream and downstream flanking regions, and versioning information for conversion of coordinates in case of updates ^[2].

The negative strand of the DNA sequence of a single gene is the complement of the positive strand. The term loses meaning for longer DNA sequences with genes on both strands. Also called the anti-sense, template, or non-coding strand (cf. positive strand).

A nested gene, or gene-within-a-gene, refers to a gene that is contained within another external host gene. Most often we find nested genes completely within an intron of, and in the opposite orientation to (i.e., positive vs. negative strand) its host gene. See Kumar (2009) for more information on nested genes.

DNA sequencing establishes the order of the bases that make up DNA. Next-generation DNA sequencing (abbreviated NGS) refers to the use of technologies for sequencing DNA that became available shortly after the completion of the Human Genome Project (which relied on the first-generation method of Sanger sequencing). Faster and cheaper than their predecessors, NGS technologies can sequence an entire human genome in a single day and for less than $1,000 ^[1]. See Part 2 of The Evolution of DNA Sequencing Technology series.

In molecular genetics/genomics, non-canonical typically refers to intron splicing site sequences that are only very rarely used. The canonical splice donor site dinucleotide sequence is GT; in rare cases, the non-canonical sequence GC is used instead (cf. canonical).

Non-coding DNA corresponds to the portions of an organism’s genome that do not code for amino acids, the building blocks of proteins. Some non-coding DNA sequences are known to serve functional roles, such as in the regulation of gene expression, while other areas of non-coding DNA have no known function ^[1].

A base or sequence which does not match the most common element found at a given position (cf. consensus sequence).

Refers to the absence of identical components; many databases have the same sequences present multiple times, but non-redundant versions are searched to save time and computing resources.

An isoform present in the target species (e.g., D. yakuba) that is not present in the informant species (e.g., D. melanogaster).

Gene models predicted by N-SCAN and transcripts assembled by TransDecoder based on RNA-Seq reads were analyzed by the Program to Assemble Spliced Alignments (PASA) pipeline to improve the accuracy of the predicted gene models. The output of the PASA pipeline consists of predictions for multiple isoforms of a gene with the locations of the 5' and 3' untranslated regions (UTRs). The PASA pipeline was originally designed to incorporate transcriptome evidence from Expressed Sequence Tags (ESTs), and the pipeline was modified to analyze RNA-Seq data.

Nucleic acids are large biomolecules that play essential roles in all cells and viruses. A major function of nucleic acids involves the storage and expression of genomic information. Deoxyribonucleic acid, or DNA, encodes the information cells need to make proteins. A related type of nucleic acid, called ribonucleic acid (RNA), comes in different molecular forms that play multiple cellular roles, including protein synthesis ^[1].

A nucleotide is the basic building block of nucleic acids (RNA and DNA). A nucleotide consists of a sugar molecule (either ribose in RNA or deoxyribose in DNA) attached to a phosphate group and a nitrogen-containing base. The bases used in DNA are adenine (A), cytosine (C), guanine (G) and thymine (T). In RNA, the base uracil (U) takes the place of thymine. DNA and RNA molecules are polymers made up of long chains of nucleotides ^[1].

An open reading frame, as related to genomics, is a reading frame that does not include a stop codon in a portion of a DNA sequence (e.g., coding exon). A long ORF is often part of a gene (that is, a sequence directly coding for a protein) ^[1].

Genes in different species that derive from a single ancestral gene in the last common ancestor of the respective species. Orthologous genes have a shared ancestry of a character or genetic region due to recent speciation ^[2].

Genes in different species that derive from a common ancestor, i.e., they are direct evolutionary counterparts ^[2].

A paralog is one of a set of homologous genes that have diverged from each other because of gene duplication. For example, the mouse α-globin and β-globin genes are paralogs. The relationship between mouse α-globin and chick β-globin is also considered paralogous ^[2].

Paralogous genes are at different chromosomal locations in the same organism and have structural similarities indicating that they derived from a common ancestral gene, but they have since diverged from the parent copy by mutation and selection or drift.

Describes the relationship of homologous genes that arose by gene duplication ^[2].

Using the simplest assumptions to explain a result.

A peptide is a short chain of amino acids (typically 2 to 50) linked by chemical bonds (called peptide bonds). A longer chain of linked amino acids (51 or more) is a polypeptide. The proteins manufactured inside cells are made from one or more polypeptides ^[1].

See "identity"

The phase describes the number of bases between the end of the exon (defined by the splice site) and the full codon nearest that splice site. The number of bases between the adjacent full codon and an exon/splice site can be 0, 1 or 2; this number is the phase. The phase of an upstream exon will determine which frame is translated in the downstream exon by indicating how many bases after the splice acceptor site are needed to create a full codon of 3 bases.

About 250 adenine (A) nucleotides that are post-transcriptionally added by poly(A) polymerase to the 3' end of eukaryotic transcripts, following cleavage of the newly synthesized RNA ~20 nucleotides downstream of an AAUAAA polyadenylation signal sequence.

Amino acid chain containing more than 50 amino acids joined together by peptide (amide) bonds.

In a gene, the DNA strand that has the sequence found in the RNA molecule; also called the sense, positive, or non-template strand.

The initial transcript from a protein-coding gene that contains both introns and exons. Pre-mRNA requires the addition of a 5' cap and 3' poly-A tail and the removal of introns to produce the final mature mRNA molecule containing joined exons.

Proteins are large, complex molecules that play many important roles in the body. They are critical to most of the work done by cells and are required for the structure, function and regulation of the body’s tissues and organs. A protein is made up of one or more long, folded chains of amino acids (each called a polypeptide), whose sequences are determined by the DNA sequence of the protein-coding gene ^[1].

Any gene whose ultimate biologically functional product is a protein.

A pseudogene is a segment of DNA that structurally resembles a gene but is not capable of coding for a protein. Pseudogenes are most often derived from genes that have lost their protein-coding ability due to accumulated mutations that have occurred over the course of evolution ^[1].

Something that may be predicted or inferred but that requires more evidence to confirm or refute.

The input sequence (or other type of search term) with which all of the entries in a database are to be compared.

RNA-Seq reads (100–125 bp in length) are derived primarily from processed mRNA (i.e., after the introns have been removed). Hence, genomic regions with RNA-Seq read coverage usually correspond to transcribed exons, which include both the translated and untranslated regions.

See "frame"

NCBI’s Reference Sequence (RefSeq) project, is a non-redundant, annotated set of sequences that serve as reference standards. They are derived from the International Nucleotide Sequence Database Collaboration (INSDC) databases and include chromosomes, complete genomes (plasmids, organelles, viruses, archaea, bacteria, and eukaryotes), intermediate assembled genomic contigs, curated genomic regions, mRNAs, RNAs, and proteins ^[2]. See O’Leary et al. (2015) for a detailed overview.

See "gene regulation"

DNA sequences that control gene expression by binding to proteins which increase or decrease synthesis of the gene product.

A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

Ribonucleic acid (abbreviated RNA) is a nucleic acid present in all living cells that has structural similarities to DNA. Unlike DNA, however, RNA is most often single-stranded. An RNA molecule has a backbone made of alternating phosphate groups and the sugar ribose, rather than the deoxyribose found in DNA. Attached to each sugar is one of four bases: adenine (A), uracil (U), cytosine (C) or guanine (G). Different types of RNA exist in cells: messenger RNA (mRNA), ribosomal RNA (rRNA) and transfer RNA (tRNA). In addition, some RNAs are involved in regulating gene expression. Certain viruses use RNA as their genomic material ^[1].

A technique which sequences RNA rather than DNA. It is most often used (in annotation) to identify genomic regions which are transcribed and present in mRNA, and thus possible exon loci.

A scaffold is an ordered and oriented set of contigs ^[2].

Shotgun sequencing is a laboratory technique for determining the DNA sequence of an organism’s genome. The method involves randomly breaking up the genome into small DNA fragments that are sequenced individually. A computer program looks for overlaps in the DNA sequences, using them to reassemble the fragments in their correct order to reconstitute the genome ^[1]. This strategy for sequencing whole genomes, pioneered by the for-profit company Celera, is prone to assembly errors.

A nucleotide repeat, with one or a small number of bases, such as AAAAAAAAAAAA or CACACACACA.

Single-nucleotide polymorphism; a difference in DNA sequence at a single base between two sequences.

GEP UCSC Genome Browser track showing the results of a spaln alignment, which here compares D. melanogaster protein sequences to the target genome; it can be thought of as similar to (though distinct from) tblastn.

Speciation is a lineage-splitting event that produces two or more separate species. See "Defining speciation" for an example ^[4].

The splicing site at the 3' end of an intron, at the boundary between an intron and the exon immediately downstream of the intron. The canonical splice acceptor site dinucleotide sequence is AG.

The splicing site at the 5' end of an intron, at the boundary between an intron and the exon immediately upstream of the intron. The canonical splice donor site dinucleotide sequence is GT; in rare cases, the non-canonical sequence GC is used instead.

Either a splice acceptor site or a splice donor site.

To cut introns out of an RNA transcript and rejoin the RNA molecule ^[4].

The process by which introns are removed and exons are joined to produce a mature, functional RNA (mRNA) from a primary transcript. Some RNAs are self-splicing, but most require a specific ribonucleoprotein complex to catalyze the reaction.

Likely occurred by chance alone and, therefore, is not evidence of real biological conservation.

The first codon of a CDS. In eukaryotes this is almost always ATG, which codes for methionine (one of the 20 amino acids).

The nucleotide at which transcription starts, usually denoted as position +1 in reference to the gene being transcribed.

A stop codon is a sequence of three nucleotides (a trinucleotide) in DNA or messenger RNA (mRNA) that signals a halt to synthesis of that copy of a (poly)peptide in the cell. There are 64 different trinucleotide codons: 61 specify amino acids and 3 are stop codons (i.e., UAA, UAG and UGA) ^[1]. Since stop codons don’t specify any amino acid, they are sometimes referred to as "nonsense codons."

The sequence, typically retrieved from a database, to which the sequence of interest (the "query") is being compared.

The order and orientation of genes in a given chromosomal region; two regions are said to be syntenic if all genes are the same, in the same order, and in the same orientation; conservation of local genomic neighborhood.

The target gene, as related to the Pathways Project, is the gene (e.g., Rheb) your instructor assigned you to annotate in a specific target species.

The target species, as related to the Pathways Project, is the species (e.g., D. yakuba) in which your instructor assigned you to annotate the target gene.

BLAST search tool in which the query is an amino acid sequence, and the subject is the six amino acid sequences translated from the six frames found in double stranded DNA. Typically used when using a protein sequence to search a nucleotide database.

BLAST version in which the query is all 6 possible amino acid sequences derived from translation of all 6 frames and the subjects are the 6 possible amino acid sequences derived from translation of all 6 frames of another nucleotide sequence. Not surprisingly, this is computationally very expensive.

Thymine (T) is one of the four nucleotide bases in DNA, with the other three being adenine (A), cytosine (C) and guanine (G). Within a double-stranded DNA molecule, thymine bases on one strand pair with adenine bases on the opposite strand. The sequence of the four nucleotide bases encodes DNA’s information ^[1].

The RNA molecule which is the immediate product of transcription of a gene, which is often modified before becoming fully functional.

The process of copying one strand of a DNA double helix by RNA polymerase, creating a complimentary strand of RNA called the transcript.

Transcription, as related to genomics, is the process of making an RNA copy of a gene’s DNA sequence. This copy, called messenger RNA (mRNA), carries the gene’s protein information encoded in DNA. In humans and other complex organisms, mRNA moves from the cell nucleus to the cell cytoplasm (watery interior), where it is used for synthesizing the encoded protein ^[1].

The process by which codons in an mRNA are used by the ribosome to direct protein synthesis.

Translation, as related to genomics, is the process through which information encoded in messenger RNA (mRNA) directs the addition of amino acids during protein synthesis. Translation takes place on ribosomes in the cell cytoplasm, where mRNA is read and translated into the string of amino acid chains that make up the synthesized protein ^[1].

The location in DNA, generally upstream of a gene’s coding sequence, where RNA polymerase begins transcription.

University of California Santa Cruz; host to a popular genome browser.

Multiple isoforms of a gene could differ only in their untranslated regions and encode the same polypeptide sequence. The term "unique isoforms" refers to the subset of isoforms that encode different polypeptide sequences of a gene. For example, if isoforms A and B use coding exons 1, 3, and 4, and isoform C uses coding exons 1, 2 and 4, then either the combination of A and C or the combination of B and C would constitute the set of unique isoforms for the gene.

Toward the 5' end of a single stranded length of DNA or gene of interest (e.g., target gene). Upstream also refers to the genomic region prior to the feature being examined (cf. downstream).

Uracil (U) is one of the four nucleotide bases in RNA, with the other three being adenine (A), cytosine (C) and guanine (G). In RNA, uracil pairs with adenine. In a DNA molecule, the nucleotide thymine (T) is used in place of uracil ^[1].

"Untranslated region"; a segment of DNA (or RNA) that is transcribed and present in the mature mRNA but is not translated into protein. UTRs may be found at either or both the 5' and 3' ends of a gene or transcript.

See "genomic variation"