Tutorials for final

Question 1

Describe microsatellites

Answer 1

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

Question 2

What do you know in there are multiple independently-derived mutants with the same phenotype?

Answer 2

has to be a mutation in the SAME gene

can be different mutations in the same gene

Question 3

Name a type of next generation sequencing

Answer 3

pyrosequencing

Question 4

What is the average read length of pyrosequencing? How many reads per run?

Answer 4

700 bp

1 million reads per run

Question 5

What is the accuracy of pyrosequencing?

Answer 5

99.9

Question 6

How long does it take to complete one run of pyrosequencing?

Answer 6

24 hours

Question 7

What are TAIR and MGI?

Answer 7

specialized databases
TAIR is for Arabidopsis
MGI is for mice

Question 8

What is blastx?

Answer 8

nucleotide query translated into all 6 reading frames against a protein database

Question 9

What is tblastn?

Answer 9

protein query, searched against a nucleotide database in all 6 reading frames

Question 10

What is tblastx?

Answer 10

nucelotide query translated to protein in all 6 reading frame searched against a nucleotide database translated in all 6 reading frames

Question 11

What is tblastx?

Answer 11

nucelotide query translated to protein in all 6 reading frame searched against a nucleotide database translated in all 6 reading frames

Question 12

What does the score tell you?

Answer 12

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)

Question 13

When a high score a better match?

Answer 13

only when comparing fragments of the same size

Question 14

How are scores given?

Answer 14

positive score for each matching pair, negative value given for each gap needed to match

Question 15

How many nucleotides are currently needed to have a unique sequence?

Answer 15

19

Question 16

What is UniGene?

Answer 16

database of the transcriptome
identifies transcripts from the same locus
analyzes expression by tissue, age and health status
reports related proteins and clone resources

Question 17

What is GEO (Gene Expression Omnibus)?

Answer 17

expression profiles
transcript-based
contains publicly available data from microarray and sequence-based gene expression profiles submitted by researchers

Question 18

What does Gene do?

Answer 18

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

Question 19

What is GEO (Gene Expression Omnibus)?

Answer 19

transcript-based

contains publicly available data from microarray and sequence-based gene expression profiles submitted by researchers

Question 20

What does Gene do?

Answer 20

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

Question 21

What does Map Viewer do?

Answer 21

provides locus information, genome mapping and sequence data

Question 22

What does Map Viewer do?

Answer 22

provides locus information, genome mapping and sequence data

Question 23

What is an ortholog?

Answer 23

genes found in different species with the same function, come from a single ancestral gene

Question 24

What are paralogs?

Answer 24

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