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20 Cards in this Set
- Front
- Back
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what are the 4 characteristics of "next generation sequencers"
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-amplification with PCR
-ligation of amplified material to a solid surface -sequencing in parallel fashion -depth/deep sequencers (more overlap of genes) |
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in 454/pyrosequencing, what type of sequencing is it
-what solid surface is used -how is DNA amplified |
sequencing by synthesis
-pico-titer plate -emulsion PCR |
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what are the 5 steps of 454/pyrosequencing
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1. single stranded DNA
2. attach adaptors to both ends of ssDNA 3. adaptors bind to beads, emulsion PCR occurs 4. beads load on pico-titer plate 5. complementary strand to the template strand is synthesized, 4 base pairs are added sequentially, incorporation of new base causes cascade of reactions that generates light that is captured by a CCD camera. Wash, repeat step 5 |
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what are the advantages and disadvantages of 454/pyrosequencing (3)
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advantage: long reads, do novo, small data files
disadvantage: analog signal, low number of bases/run, expensive |
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what type of sequencing is solexa
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sequencing by synthesis (similar to 454/pyrosequencing)
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what is the process of amplification in solexa
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1. immobilize DNA to Flow Cell (bind ssDNA to flow cell surface)
2. Bridge amplification (creates dsDNA) 3. Cluster Generation (denature dsDNA, forming clusters on Flow Cell surface) |
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what is the process of sequencing after amplification in solexa
-how are bases identified |
1. add 4 color reversible terminators
2. image fluorophore 3. remove/wash 3' block and fluorophore 4. add next base -identity of each base at each cluster is read off from sequential images |
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what are the advantages and disadvantages of solexa (3)
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advantages: high number bases/run (Gb), low cost, resequencing applications
disadvantages: short reads (microreads), no de novo, 3 days/run |
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in whole genome shotgun method, what are contigs (continuous fragments)
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overlapping fragments that altogether form a continuous DNA molecule
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what is pair-end sequencing
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recognizes specific sequences and cuts further down from them
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what is the definition of functional genomics
-how has science shifted in its approach to analyzing genes |
study of gene functions
-more focus on entire genome and interrelationships rather than on specific genes/proteins |
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what is bioinformatics
-important database? |
computer-based technology that organizes, shares, analyzes genome
-GenBank |
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what is annotation
-two methods useful in annotation |
process of identifying genes, their regulatory sequences, and their functions
-ORF, BLAST |
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what is ORF
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sequences of nucleotides that actually encode for a protein (protein-encoding gene)
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what is BLAST
-what does it help us identify |
compares a segment of DNA with a known sequence
-allows us to identify homologous genes that evolutionary-related |
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what is sequence analysis
-two types with their examples |
gene sequence/trends that are used to predict polypeptide/protein function
-protein domains: ions channels, membrane-spanning regions, secretion, export -protein motifs: helix-turn-helix, leucine zipper, zinc finger |
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How are protein DNA interactions identified
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ChIP, ChIP-on-ChIP
-identifying genes that are regulated by DNA-binding transcription factors (genes regulated by proteins) |
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what is 2DGE
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separtes proteins with electrophoresis
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define interactome
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(systems biology) elucidates interacting pathways and interrelationships of molecules/genes/proteins using genomic research
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what are network maps
-why are they important |
sketches illustrating the interactions of genes, proteins
-used in drug discovery/development, human disease |
