Genom glossary
Genom glossary
Genom glossary
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Flashcards
• The process of classifying reads or contigs into different groups or taxonomies.
• Various measurements of the environment where the metagenomic sample was collected.
• branch of science that encompasses the description, identification, nomenclature, and classification of organisms
• Direct sequencing of environmental DNA• Study of two aspects: taxonomic content (who is there?) and functional content (what can they do??)
• Also called targeted sequencing of marker genes• Study of selected marker gene(s) after PCR amplification from environmental DNA.
• Study of total (microbial) RNA from environmental samples.
• Also called community genomics• Study of metagenomes, genetic material recovered directly from environmental samples.• Seeks to understand microbial ecosystems by studying the genomic content of the constituent microbes in their natural community setting.
• 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.• Provides insight into “evolutionary innovation”(adapting a pre-existing gene product for a new function).
• Sequences are direct descendants of a sequence in a common ancestor.• 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.• Most likely have similar domain structure, three-dimensional structure, and biological function.
• Shared ancestry between protein or DNA sequences.• Genes are or are not homologous (not measured in degrees)
• Quantitative measure of relatedness between nucleotide or amino acid sequences (% sequence identity).• Allows quantifying changes that occur as two sequences diverge (e.g. substitutions, insertions, deletions).• Identification of residues crucial for maintaining a protein’s structure or function.• High degrees of sequence similarity might imply a common evolutionary history and possible commonality in biological function.
• Structured system of controlled vocabularies.
• A measure that reflects bias for guanine bases on the leading strand of DNA and cytosine bases on the lagging strand.
Core genome
• Genes present in all strains
• Percentage of guanine and cytosine residues within a genome.
• A variation between two genomes that involves a single base pair.
• A genome that went through the finishing stage, and is a complete representation of all DNA sequences in the sequenced organism.
• The final phase in a genome-sequencing project, in which all gaps between contigs are closed and all ambiguities are resolved. This is much more labor-intensive than the shotgun phase, so the sequencing of many genomes is now left unfinished.
• A genome that has been assembled into a number of contigs. Gaps can represent variable amounts of missing information.
• A set of contigs ordered by linking information.
• The length such that 50% of the assembled genome lies in blocks of the N50 size or longer.
• The average number of reads representing a given nucleotide in the reconstructed sequence.
• Set of overlapping DNA segments derived from a single genetic source.
• The most common nucleotide or amino acid at a particular position after multiple sequences are aligned.
• Computer program for identifying a nucleobase sequence from "trace" data generated by an automated DNA sequencer.
• The total number of reads obtained from the sequencing process.• The total number of bases (number of reads * read length) obtained from the sequencing process.
• The result of sequencing a library of DNA fragments.
• A collection of DNA fragments with adapters ligated to each end.
• The application of genome sequencing to a close relative of a strain that has already been sequenced. The availability of a template genome greatly facilitates the finishing stage of sequencing. In contrast to resequencing, de novo sequencing, in which a large proportion of the genome is novel sequence, is much more challenging.
• Method used for sequencing long DNA strands. It is named by analogy with the rapidly-expanding, quasi-random firing pattern of a shotgun.
• The process of attaching biological information to sequences.
• The process of taking a large number of short DNA sequences and putting them back together to create a representation of the original chromosomes from which the DNA originated.
• Scientific endeavor that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaeon, a protist or a virus) and to annotate protein-coding genes and other important genome-encoded features.
• The uptake of DNA from the environment by bacteria.
• The transfer of DNA between cells via a phage vector.
• The transfer of DNA by direct cell-to-cell contact often mediated by conjugative plasmids.
• Number of plasmids per chromosome unit.
• Region required for the replication of plasmids.
• Self-replicating information carrier that is independently separated over daughter cells. Plasmids can be eventually self-transmitting.
• Acts to remove deleterious alleles from the population.
