24 - BIOINFORMATICS AND GENOMICS Flashcards
what is forward genetics
phenotype to genotype
what is reverse genetics
genotype to phenotype
how do we start looking at the DNA sequences, what is the first step?
look for sequences associated with protein encoding genes
look for ORFs (stretches of codons that are not stop codons) as evidence of possible exons/genes and predict if they can be exons
how are exons determined from ORFs
check it against genomes that you already have the data about, and if there is high conservation that indicates the chosen ORFs are exons
how can cDNA be used to determine whether the ORF is part of a real gene
cDNAs come from mRNAs, which means those sequences were transcribed
what are other sequence features associated with the presence of a gene
how can “codon bias” provide evidence that an ORF is part of a real gene
distribution of different types of sequences in the human genome
why is 3% of the genome exons, but only 1% is protein coding?
due to 3’ and 5’ UTRs
part of exons but are beyond the start and stop codons, do not code for a protein
beyong protein encoding genes, what is the rest of the genome doing?
what is ENCODE and what is its goal
encyclopedia of DNA elements
the goal is to identify all functional elements within the human genome
what are the different comparisons that can be made in comparative genomics?
how can we test for whether a conserved non coding sequence might be a regulatory element
how can we use a transgenic reporter to determine whether a conserved non coding sequence across species is a functional element
observation: ultraconserved non coding sequence from the human ISL1 gene can recapitulate expression of the mouse ISL1 gene during embryogenesis
this element is a regulatory elements controlling expression of ISL1 gene in both mouse and humans
how can we compare genomes between species to find differences between species (example of chimps and macaques deleted sequence in humans)
results: this enhancer can drive the expression in two different structures that are present in mammals like mice and chimps but are absent in humans
interpretation: loss of an ancestral vibrissae/penile spine enhancer in humans is correlated with corresponding loss og sensory vibrissae and penile spines
what is synteny
the conserved order of genes between two genomes
similarities in genome organisation
example of synteny and the interpretation of that between mice and humans
