Tutorials for final Flashcards
(24 cards)
Describe microsatellites
short simple sequence repeat frequent in the human genome (~every 30000bp) 1-5bp long tandem repeats of 15-100 copies mutate by replication error highly polymorphic
What do you know in there are multiple independently-derived mutants with the same phenotype?
has to be a mutation in the SAME gene
can be different mutations in the same gene
Name a type of next generation sequencing
pyrosequencing
What is the average read length of pyrosequencing? How many reads per run?
700 bp
1 million reads per run
What is the accuracy of pyrosequencing?
99.9
How long does it take to complete one run of pyrosequencing?
24 hours
What are TAIR and MGI?
specialized databases
TAIR is for Arabidopsis
MGI is for mice
What is blastx?
nucleotide query translated into all 6 reading frames against a protein database
What is tblastn?
protein query, searched against a nucleotide database in all 6 reading frames
What is tblastx?
nucelotide query translated to protein in all 6 reading frame searched against a nucleotide database translated in all 6 reading frames
What is tblastx?
nucelotide query translated to protein in all 6 reading frame searched against a nucleotide database translated in all 6 reading frames
What does the score tell you?
how many hits there were
the longer the sequence the higher the potential score
ie 800/1000= 800 score
but 100/100= 100 score (more accurate)
When a high score a better match?
only when comparing fragments of the same size
How are scores given?
positive score for each matching pair, negative value given for each gap needed to match
How many nucleotides are currently needed to have a unique sequence?
19
What is UniGene?
database of the transcriptome
identifies transcripts from the same locus
analyzes expression by tissue, age and health status
reports related proteins and clone resources
What is GEO (Gene Expression Omnibus)?
expression profiles
transcript-based
contains publicly available data from microarray and sequence-based gene expression profiles submitted by researchers
What does Gene do?
looking at a specific gene, integrating info from different species
integrates information from a variety of species
may include nomenclature, reference sequences, maps, pathways, variations, phenotypes, and links to genome, phenotype and locus-specific resources
What is GEO (Gene Expression Omnibus)?
transcript-based
contains publicly available data from microarray and sequence-based gene expression profiles submitted by researchers
What does Gene do?
integrates information from a variety of species
may include nomenclature, reference sequences, maps, pathways, variations, phenotypes, and links to genome, phenotype and locus-specific resources
What does Map Viewer do?
provides locus information, genome mapping and sequence data
What does Map Viewer do?
provides locus information, genome mapping and sequence data
What is an ortholog?
genes found in different species with the same function, come from a single ancestral gene
What are paralogs?
two or more genes in the same species that are so similar they are thought to have arisen from a single ancestral gene, however they now have different functions