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20 Cards in this Set

  • Front
  • Back
what are the 4 characteristics of "next generation sequencers"
-amplification with PCR
-ligation of amplified material to a solid surface
-sequencing in parallel fashion
-depth/deep sequencers (more overlap of genes)
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
what are the 5 steps of 454/pyrosequencing
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
what are the advantages and disadvantages of 454/pyrosequencing (3)
advantage: long reads, do novo, small data files
disadvantage: analog signal, low number of bases/run, expensive
what type of sequencing is solexa
sequencing by synthesis (similar to 454/pyrosequencing)
what is the process of amplification in solexa
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)
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
what are the advantages and disadvantages of solexa (3)
advantages: high number bases/run (Gb), low cost, resequencing applications
disadvantages: short reads (microreads), no de novo, 3 days/run
in whole genome shotgun method, what are contigs (continuous fragments)
overlapping fragments that altogether form a continuous DNA molecule
what is pair-end sequencing
recognizes specific sequences and cuts further down from them
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
what is bioinformatics
-important database?
computer-based technology that organizes, shares, analyzes genome
what is annotation
-two methods useful in annotation
process of identifying genes, their regulatory sequences, and their functions
what is ORF
sequences of nucleotides that actually encode for a protein (protein-encoding gene)
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
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
How are protein DNA interactions identified
ChIP, ChIP-on-ChIP
-identifying genes that are regulated by DNA-binding transcription factors (genes regulated by proteins)
what is 2DGE
separtes proteins with electrophoresis
define interactome
(systems biology) elucidates interacting pathways and interrelationships of molecules/genes/proteins using genomic research
what are network maps
-why are they important
sketches illustrating the interactions of genes, proteins
-used in drug discovery/development, human disease