Halorhabdus utahensis Genome

This page will be used by Davidson College students in the Genomics Laboratory course.

RNA Genes

tRNA Genes Check List
rRNA operon
2 misc. RNA genes (short summary list)
References
Gene Annotation Template
General Questions
Page for Annotated Genes

Other Resources

Consensus Shine Dalgarno Excel File for H. utahensis
Tutorials for annotating genomes

1. Will DeLoache- BioPerl Installation
   
2. Pallavi-Conserved Domains Database (CDD)
   
3. Mary- Protein Data Bank
   
4. Laura Voss - Pfam Database
   

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This is a list of glossary words (A - Z):

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

C

carbon fixation - using carbon dioxide to create organic materials [1] (Samantha)

chemotaxis - the process in which cells will seek out or flee from a high concentration of certain chemicals and is found in both uni- and multicellular organisms. This process is used to avoid toxins or find food in unicelllular organisms or tasks such as reproduction in multicellular organisms [2] (Nick)

COG (Cluster of Orthologous Groups)- corresponds to a highly conserved domain and generally consists of either individual proteins or groups of paralogs (COG Pallavi)

concatemer - long continuous DNA molecule that contains the same DNA sequence repeated in series [3](Samantha)

coverage - refers to the number of times, on average, any piece of DNA in a sequenced genome has been individually sequenced (Lecture, Jay)

F

FASTA format - a format used to convey either nucleic acid sequences or peptide sequences, in which base pairs or amino acids are represented by single-letter codes. The sequence name and other descriptors often precede the amino acide sequence. [4] (Nick)

finished genome - a genome that has been sequenced at least partly by hand, resulting at least 99.99% sequence accuracy (Lecture, Jay)

G

glaucophyte - freshwater algae that have not been studied well [5](Samantha)
GC Content - the percentage of bases within a certain sequence of DNA (e.g. a gene or a genome) that are either guanine or cytosine; a higher GC content is characteristic of a coding region of a gene; differences in GC content between a gene and a genome can be used as evidence for horizontal gene transfer [6] (Matt)

H

haemolysin or hemolysin - a chemical produced by a bacteria that causes lysis of red blood cells [7] (Nick)

halophile - an organism, most often of the Archaea domain, that lives in environments containing high concentrations of salt [8] (Matt)

haplotype-collection of alleles that travel together (Lecture, Pallavi)

haptophyte - phylum of algae [9](Samantha)

heterokont - major line of eukaryotes consisting of about 10,500 known species, most of which are algae [10](Samantha)

homeobox - DNA sequence within transcription factor genes that allow the cell to respond to patterns of development by having the transcription factors switch on gene cascades [11](Samantha)

horizontal gene transfer-DNA transmission between species and incorporation of the DNA into the recipient's genome (horizontal gene transfer Pallavi)

hydrolase - an enzyme that catalyzes hydrolysis, the breakdown of water into oxygen and hydrogen atoms which often take part in subsequent reactions [12] (Nick)

I

indole-a chemical compound that is produced from the break down of tryptophan (indole Pallavi)

inclusion body - Inclusion bodies are collections of stainable substances, usually proteins, that are found either in the nucleus or the cytoplasm. It is thought that these bodies are often the result of viral proteins that misfolded [13] (Nick)

isoelectric point - the pH at which a molecule is neutral [14] (Nick)

M

mycoplasma - genus of bacteria that lack a cell wall [15] (Nick)

N

nucleomorph - reduced eukaryotic nuclei found in plastids [16](Samantha)

O

open reading frame (ORF)-a segment of DNA that can potentially encode for a protein and it begins with a start codon (usually ATG) ORF (Pallavi)

operon - a segment of DNA involving an operator, promoter, and one or more genes that operate as a single unit during transcription [17] (Nick)

optical mapping-DNA sequences of the organism in question are compared against a karyotype that specifically looks at restriction sites found within the DNA to correctly order the DNA sequences on a chromosome. This methodology gives very detailed haplotype information and allows for the detection of sequence variations across an entire genome optical mapping (Pallavi)

ortholog-different DNA sequences that look very similar, but have no evolutionary relationship (Lecture, Pallavi)

oxidoreductase - an enzyme that catalyzes redox reactions by transferring electrons from one molecule (the reductant) to another (the oxidant) [18] (Nick)

P

paralog-identical DNA sequences within a species (Lecture, Pallavi)

phylogenetic tree - a diagram showing the evolutionary relationships between biological species that are thought to share a common ancestor [19] (Nick)

plastid - major organelles in plants or algae [20](Samantha)

proteome - entire set of proteins expressed by a genome, cell, tissue, or organism. It may refer to expressed proteins under certain conditions [21](Samantha)

psuedogenes-A sequence of DNA that looks like a gene, but most likely contains many stop codons. It may have evolved away from a real gene or a paralog might have taken its place (Lecture, Pallavi)

R

rDNA-These are DNA sequences that encode for ribosomal RNA. Note that rDNA can also stand for recombinant DNA. (rDNA Pallavi)

retrotransposons - RNA transcribed back into DNA and added into the genome [22](Samantha)

S

Serovar-a subdivision of a species based on the characteristics of their cell surface antigens (serovar Pallavi)
scaffold - a section of a sequenced genome composed of contigs that are in the right order but not necessarily connected (MedTerms Dictionary, Jay)
Shine-Dalgarno sequence - A ribosomal binding site on an mRNA, usually a sequence of six base pairs about six or seven base pairs upstream of the start codon. An anti-Shine-Dalgarno sequence exists on the rRNA in the small subunit of the ribosome; when the two sequences align, the mRNA is lined up and prepared for transcription. (Lecture and Wikipedia article, Laura)
Note: The Shine-Dalgarno consensus sequence for our genome is TAGGAGG.
signal peptide - a short peptide chain that directs the post-translational transport of a protein [23] (Matt)
synteny - a neologism from the Greek for "on the same ribbon". Genes that are syntenic in one species are on the same chromosome; genes that are syntenic across species retain the same order on respective chromosomes as a result of descent from a common ancestor (Answers.com, Jay)

T

transposons / transposable elements - DNA sequences that can move around to different positions in a single cell's genome. Transposons can cause mutations and change the length of the genome. [24](Samantha)
Transposon Mutagenesis-a procedure in which a transposon is inserted into a gene, which inactivates the gene and can lead to the discovery of the phenotype associated with this gene (transposon mutagenesis Pallavi)

W

whole genome shotgun sequencing - a method of sequencing where DNA is cut into small pieces and cloned into vectors, then both ends of every vector are sequenced in about 500 bps to form mate pairs. Mate pairs rarely overlap, but are used to reassemble the sequence using software. [25](Samantha)

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