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211 Cards in this Set
- Front
- Back
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Alanine
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A
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Arginine
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R
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Asparagine
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N
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Aspartic Acid
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D
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Cysteine
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C
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Glutamic acid
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E
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Glutamine
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Q
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Proline
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P
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Serine
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S
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Threonine
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T
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Tryptophan
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W
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Tyrosine
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Y
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Valine
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V
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Unknown
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X
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Glycine
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G
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Histidine
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H
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Isoleucine
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I
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Leucine
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L
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Lysine
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K
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Methionine
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M
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Phenylalanine
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F
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Purine
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R
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Pyrimidine
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Y
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G or A
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R
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T or C
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Y
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Amino
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M
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A or C
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M
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Keto
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K
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G or T
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K
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Strong
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S
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G or C
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S
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A or T
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W
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Weak
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W
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Not G
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H
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Not A
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B
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Not T
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V
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Not C
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D
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What was Sanger sequencing invented?
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1977
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What is the difference between a transcriptome and a proteome?
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Transcriptome is the entire set of transcribed sequences produced by the genome whereas a proteome is the entire set of proteins encoded by the genome.
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Two traits are homologous if...
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they are derived from a common ancestor.
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T/F. Homology can be measured.
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F
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What is homoplasy and is it common?
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Independent origin of similar characters between species. Yes.
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Wings and feathers are an example of which character state for birds?
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apomorphy
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Human speech is an example of which character state?
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autapomorphy
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Possession of vertebrae in zebras, orangutans and cheetahs is an example of which character state?
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plesiomorphy
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An example of __________ is the five toes seen on the hind legs of rats and apes. This character-state originated very early in Tetrapoda and occurs in other tetrapod groups, e.g. in lizards
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symplesiomorphy
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Which character state allows for phylogenies to be built?
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synapomorphy
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How many possible transversions are there?
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8
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How many possible transitions are there?
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4
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What do the 4 aliquots in Maxam & Gilbert sequencing detect?
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G, A&G, C&T, C
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What is the limitation for Maxam and Gilbert sequencing?
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requires a cloning step (amplification and labeling)
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T/F. Maxam and Gilbert sequencing is allowed to go to completion.
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F
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T/F. Sanger sequencing requires primers.
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T
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Which sequencing method uses dideoxyriboneucleotide triphosphates?
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Sanger
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What do Sanger and Maxam & Gilbert sequencing have in common?
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radiolabels, gel electrophoresis, autoradiography
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How does Sanger affect DNA replication?
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ddNTPs stop DNA replication at different sites
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Is it more efficient to use flurophores or radiolabelling for Sanger sequencing? Why?
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fluorophores, only 1 lane needed, can use capillaries and a laser, fluorescence recorded in a graph and read by a computer
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Why are Sanger samples bad at the end of a trace?
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fluorophores are dying
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Why are Sanger samples bad at the beginning of a trace?
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primers show up in the trace
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What is the main issue with Sanger sequencing? How can this be avoided?
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stacking of nucleotides; try to sequence the other strand
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T/F. Purines stack more than pyrimidines.
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T
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A probability of 1% error has a Phred score of ____.
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20
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A Phred score of 30 indicaties a probability of ____ error.
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0.1%
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Which type of sequencing inserts genome fragments into BACS?
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hierarchical sequencing
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What are some advantages of shotgun sequencing?
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Can use computers instead of people; sequence in both directions to overcome stacking; assembly of all reads simultaneously
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What are some disadvantages of shotgun sequencing?
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mask repeats such as LINES, SINES, microsatellites etc
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Contigs can be assembled into ___ on the chromosome during Sanger sequencing.
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scaffolds
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T/F. Contig is another word for scaffold.
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F.
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What is the role of FrameD?
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makes guesses about the role of DNA
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How does alpha-satellite data relate to sequencing?
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we have lots of it, can be repeated up to 10 million times in a row in Drospophila therefore we don't sequence this none of the currently "complete" eukaryotic genomes are actually complete, often not found in prokaryotes
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Where do alpha-satellite repeats often occur?
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heterochromatin (centromeres and telomeres)
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What began the revolution in sequencing leading to NGS?
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pyrosequencing
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Which aspect of DNA replication does pyrosequencing make use of?
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The pyrophosphate released as the DNA strand grows
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What turns pyrophosphates into ATP?
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sulfurylase
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Which gene causes fluoresces in the presence of ATP? Which sequencing technique makes use of this?
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luciferase; 454
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What is emPCR? Which sequencing method makes use of this?
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adapters added to both ends of DNA frags, adapters attached to beads, oil added (emulsion mixture), water droplets contain only 1 bead and 1 gene, PCR occurs in each droplet, replicated DNA cannot escape due to oil, millions of PCRs in one tube, beads put on plate, 1 bead in each well, sulfurylase and luciferase added, nuc washed over, camera takes a picture, rinse plate, add next nuc. etc; 454
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What is a problem with 454?
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Hard to tell if there were 2 of the same nucleotide in a row
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Which method replaced 454?
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Illumina Solexa
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Compare terminator nucs and ddNTPs?
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Both interrupt DNA replicaiton hoewever terminator nucs are reversible.
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Which sequencing method makes use of bridge amplification?
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Illumina Solexa
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Describe the illumina solexa technique.
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DNA fragmented, adapters ligated to both ends of ds DNA frags, dense lawn of oligos on slide bind to adapters of ss frags, nucs and enzyme added,frags extended to create copies, frags clonally amplified,, DNA denatured (no more bridges), all 4 fluorescently labelled terminators are added, primers and polymerase, laser excitation, camera captures fluorescence from each cluster, rinse plate, add next terminator, etc.
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What is a problem with illumina solexa?
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analyzing data is a nightmare (look through sequential pictures)
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T/F. Nucleotide runs create a problem for both 454 and illumina solexa.
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F. Only a problem for 454
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Which sequencing method has the following steps: library preparation, cluster generation, sequencing.
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Illumina Solexa
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Explain the SOLiD system.
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DNA sheared to desired size, adapters are ligated to ends of desired frags, each fragment hybridized to a bead, emPCR, beads attached to glass slide, universal primer, di-base probes and ligase added, probe hybridizes to template and is ligated, fluorescence measured, dye cleaved off, leaving free 5' phosphate for further reactions, 7 cycles, primer reset (1 base shift)
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Which sequencing detects 2 nucleotides at a time?
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SOLiD
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T/F. 454 has high throughput.
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F
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You want to sequence a short fragment. Would you use Sanger or 454. For a long fragment?
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Sanger; 454
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What has a higher read length, 454 or lllumina?
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454
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Which uses more lanes per cell, 454 or Illumina?
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454
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Is it best to sequence short fragments with 454 or Illumina?
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Illumina
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What is more accurate, SOLiD or Illumina?
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SOLiD
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T/F. Illumina and SOLiD have long read lengths.
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F
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Which sequencing technique makes use of the H+ released as the DNA strand grows?
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Ion Torrent
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Describe Ion Torrent Sequencing.
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amplify on beads, flow nucs. one at a time on a semiconductive plate, measure electricity when H+ is released, no signal if the nucleotide is not a match.
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T/F. Ion Torrent sequencing has similar limitations to 454.
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F
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Which sequencing technique follows a single polymerase as it sequences just one template?
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Pacific Biosci
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T/F. A limitation of Pacific Biosci sequencing is amplification.
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F
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What is a pro and a con of Pacific Biosci sequencing?
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long reads; high error rate (single molecule)
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Which sequencing techniques allows you to determine the sequence and the speed of sequencing?
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Pacific Biosci
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What are microarrays used for?
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determining gene expression for many genes at once
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Describe microarrays.
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hybridixation of cDNA from a sample onto a slide spotted with probes, fluorescence intensity reflects level of gene expression
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Which sequencing method sequences cDNA?
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RNA-sequencing
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Which sequencing method found genes that were not previously there?
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RNA-sequencing
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Which sequencing method found that some gene annotations were incorrect?
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RNA-sequencing
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T/F. Microarrays give absolute gene expression values.
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F. only relative
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Which sequencing method gives you absolute values of gene expression?
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RNA-sequencing
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Name the 3 nucleotide sequence dbs.
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EMBL-EBI, NCBI, DDBJ
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Which db is responsible for the accessibility of GenBank?
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NCBI
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What does NCBI stand for?
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national center for biotechnology information
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T/F. There has been an exponential growth in data due to sequencing centers.
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T
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T/F. NCBI is curated.
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F ***
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Which db has a collection of 3D structures of proteins and nucleic acids?
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RCSB PDB
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What does RCSB PDB stand for?
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research collaboratory for structural bioinformatics protein databank
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What does an RCSB PDB entry include?
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summary of 3D structure. methods used to id structure, details on sequence, geometry details
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Which db documents protein families, domains and sites?
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InterPro
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Name the db of protein domains, families and functional sites.
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Prosite
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What is the Gene Ontology Project?
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aim to assign info about a gene product using a controlled vocab
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T/F. The Gene Ontology Project uses curated evidence.
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T
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T/F. Swiss-Prot is curated.
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T
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What does OMIM stand for?
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online medelian inheritance in man
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Name a catalog of human genes and genetic disorders.
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OMIM
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PFAM??
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????
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What does KEGG stand for?
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Kyoto Encyclopedia of Genes and Genomes
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Which db contains info on chemical reactions?
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KEGG
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Which db contains info on pathways?
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KEGG
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Who developed Entrez?
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NCBI
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Which db allows the access of data domains, nucleotide and prot sequs, complete genomes and 3D structures?
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Entrez
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What is the goal of Entrez?
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identify a representative, well-annotated mRNA sequence record
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Which db contains seqs from GenBank, RefSeq and PDB?
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Entrez
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Why is it important to refine Entrez searches?
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contains sequences from many other dbs (not all are curated) therefore quality varies, can be a high degree of redundancy
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Which option would allow you to restrict your Entrez search to entries from RefSeq only?
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"limits"
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Which Entrez link allows you to find variations in your gene of interest?
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SNP
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What does it mean if the "structure" link is not present in an Entrez entry?
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no 3D protein structure record associated
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Which sequencing method is a cheaper but effective alternative to whole genome sequencing?
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exome sequencing
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What is the goal of exome sequencing?
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selectively sequence coding regions of the genome
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Which method combines exome sequencing and RNA sequencing?
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RNA captureseq
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Which sequencing technique uses tiling arrays?
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exome sequencing and RNA CaptureSeq
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Which technique is best at sequencing rare transcripts?
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RNA CaptureSeq
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Which chemical changes cytosines to uracils?
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bisulfite
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T/F. Methylated cysteines are easily de-aminnated.
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F. they resist it
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About how much does a disposable sequencer cost?
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$900
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Which sequencing technique generates the most yield per run?
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Illumina
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Which has the best accuracy, Illumina, ion torrent or pacbio? Which has the worst?
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Illumina; Pacbio
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Which has the highest read length, Illumina, ion torrent or pacbio? Which has the worst?
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Pacbio; Illumina
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What does EMBL-EBI stand for?
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European Molecular Biology Laboratory - European Bioinformatics Institute
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T/F. EMBL is redundant.
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T?
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Which db gives term info, ancestor chart, ancestor tablem child terms, protein annotation and statistices?
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gene ontology
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What does the P code of GO indicate? The I code?
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part of; is a
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T/F. Swissprot is curated.
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T
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Which db includes sequence data, references and taxonomic data?
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Swissprot
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Which has higher quality, PfamA or B?
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A
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Which db collects protein families based on protein domain and represents them by multiple alignments?
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Pfam
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Which db has HMM logos?
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Pfam
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T/F. GenBank displays homology information.
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F
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What was GenBank developed for?
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a single nucleic acid sequence
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T/F. The GenBank locus name is unique.
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T
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T/F. Accession numbers change as entries are updated.
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F
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Which part of a GenBank entry changes as an entry is updated?
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GI number
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What designates the end of an entry in GenBank?
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//
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T/F. Genbank format can display more than one gene in a single sequence.
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T
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What is the difference between the EMBL and GenBank formats?
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EMBL is the same as GenBank format but with 2 letter codes (ex. AC = accession number)
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What is the simplest format used?
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FAST / Pearson
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T/F. FASTA files store feature information.
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F
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In which file does a sequence start with a > ?
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FASTA
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Which format is adapted for high-throughput short reads?
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FASTQ
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What do FASTQ sequences start with?
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@
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Which format stores Phred scores?
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FASTQ
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Which format can store alignment information, has 2 different formats and can contain many sequences/taxa at once?
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Phylip
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Which format was made to be read by computers?
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Abstract syntax notation (ASN1)
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Which file stores 3D position of each aa, primary and secondary structures and crystallographic experiemnts?
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PDB
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L 9 10 11 12
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go through fcs, go through practice probs
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What does COSMIC stand for?
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catalogue of somative mutations in cancer
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What does BGI stand for?
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Beijing Genomics Institute
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What is the aim of the ENCODE project?
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describe all functional elements encoded in human genome
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T/F. Locus IDs change with revisions.
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T
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How many translation tables does NCBI deal with?
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18
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Which software program performs statistical phylogenetic inference and molecular evolutionary analyses?
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PAML
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If p <0.05, is the protein under positive or negative selection?
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positive
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Which is a useful db of homology genes?
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HomoloGene
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T/F. Homology implies similarity and vice versa.
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F
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How can homologous sites be identified?
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through alignment
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What is a caveat of dot plots? How can this be solved?
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only 4 nucs therefore many dots; divide sequences into words (identity plots)
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What are the benefits of using words in a dot plot?
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can align distantly related species, can find repeat elements
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Was there a deletion in sequence 1 or 2? \ .......................................................\
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1
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What is the highest value for a NW algorithm?
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8
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What does it mean if you skip a row or column while doing a NW algorithm?
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gap
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What is a global alignment?
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try to align all of sequence 1 with all of sequence 2; short or highly similar sequences may be missed
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Which algorithm allows the creation of local alignments?
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Smith Waterman
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What is the main diff. between SW and NW?
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SW assigns negative weight to mismatches and/or gaps
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What do local alignments try to maximize?
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number of nucleotide matches for the substrings
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Which type of alignment is more likely to identify a homologous region in catalytic domain?
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global
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What should have a greater penalty, a gao or a substitution?
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gap
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What does a gap correspond to?
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an indel
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Is it better to have staggered or consecutive gaps?
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staggered
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Does MM do a local or global alignment?
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global
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T/F. It is often useful to change cds DNA to its protein sequence first when doing alignments.
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T
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How can you test alignment significance?
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permutation test (randomly arrage one seq, align them, repeat)
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When should gaps not be penalized?
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When 2 seqs have no obvious relationship at either end
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Which alignment method is preferred when using two known to be homologous sequences?
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global
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T/F. An optimal alignment is statistically significant.
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F
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T/F. An alignment demonstrates honology.
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F. not necessarily, demonstrates similarity though
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What can multiple sequence alignments be used for?
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contig assembly, phylogenetic reconstructions, pattern finding
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Which methods to multiple sequence alignments use?
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heuristic and probabilistic
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For multiple alignments, computational time required grows as ____.
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number of nucleotides x number of sequences grows
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Which method uses pairwise alignments of all sequences and uses a distance matrix to contruct a phylogenetic tree.
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Progressive global alignment
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T/F. The tree has a strong influence on alignment.
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F
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Should you use a clustal tree for your studies
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No
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Which method aligns subgroups in a global alignment?
|
iterative global alignment
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What is MUSCLE?
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iterative global alignment
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Does Clustal include gaps?
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No
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