QUIZ: Identifying regulatory elements in bacterial genomes

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Undergraduate Bioinformatics (Bacterial Genomics - Mark Paget) FlashCards sobre QUIZ: Identifying regulatory elements in bacterial genomes, criado por Thomas Welford em 12-03-2014.
Thomas Welford
FlashCards por Thomas Welford, atualizado more than 1 year ago
Thomas Welford
Criado por Thomas Welford mais de 10 anos atrás
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Resumo de Recurso

Questão Responda
What is does the sigma factor do in the 'Transcription cycle in bacteria'? Protein needed for the initiation of RNA synthesis, allows binding between RNA polymerase to gene promoters
What is the consensus sequence? The bases that appear most often in the promoter collection
Where do the sigma factors interact with the DNA? -10 and -35 hexametric elements
Where do repressors and activators bind? (picture)
Where do repressors and activators bind? Activators bind upstream or partially overlapping region (-35 region) Repressors usually bind overlapping or downstream from promoter region
Where do most searches for regulatory elements focus on? <300bp upstream of translation start
How is transcription initiation controlled? each regulator controls a regulon e.g. Lac I controls lac operon (one or two other genes)
What does the E.coli transcriptional network look like?
What is a DOR? Dense Overlapping Regulons A set of regulators control a group of target genes, where each gene is controlled by two or more of the regulators
What is a DOR (picture)?
Why are most DNA binding sites bipartite? So can bind to more parts of the DNA
What do the bipartite DNA binding sites recognise? Dyad sequences (highly conserved) that are separated by a non-conserved spacer
What does the interaction between a DNA binding complex and a dyad sequence look like?
Do most sites match the consensus sequence? NO - most regulators bind to a range of sites and have a range of affinities
How do you represent DNA motifs? Visually - WebLOGO Sequence Patterns Position Specific Weighted Matrices (PSWM)
How do 'sequence patterns' work? String of sequence using four nucleotides Variation captured using IUPAC codes
What is a disadvantage of sequence patterns? Does not capture quantitative information on a particular position
How do you conduct a PSWM? Capture frequency of nucleotides at each position
What is the IUPAC? Code for representing degenerate nucleotide sequence patterns
What is a DNA sequence motif? Short reoccurring patterns in DNA
How do you conduct a PSSM? Start with data used to create consensus Related sites discovered using a search engine Align sequences then score each position Introduce pseudo counts Introduce background frequency
What do 'pseudocounts and background frequency of particular nucleotide in genome' solve? Product of score for each does not equal 0 Score does not account for background GC content of genome
What is the formula used to work out PSSM? Score (position, nucleotide) = (q+p) / (N + B) q=observed counts for nucleotide p=weighted pseudocounts=B*(overall frequency of nucleotide) B = total number of allocated pseudocounts N = total number of sequences (max number of observed counts) TOTAL SCORE = PRODUCT OF SCORE AT EACH POSITION
How do we identify regulatory motifs? 1) Intra-genome searches for conserved motifs - DYADS 2) Inter-genome alignments of orthologues
What do the approaches for 'identifying regulatory motifs' rely on? most DNA binding proteins bind to related sequences - SPECIFICALLY
When conducting an intra-genome search for dyads, what do we search for? W1 NX W2 W1 = 3-5 nt sequence NX = spacer with any nucleotide of X nt length W2 = 3-5 nt sequence
What are "intra-genome searches for dyads" limited to ? <300bp from translation start point
For "Intra-genome searches for dyads" what does statistical significance depend on? Length and GC content of Dyad Context of search e.g. length and GC content of upstream regions
What happens following identification of groups of significant dyads? cluster into subgroups based on conservation in surrounding nucleotides
What can a PSSM be used for within Intra-genome searches for dyads ? Search for additional targets
What is an "Inter-genome comparison of - orthologues"? Genome sequences of groups of related but distinct (e.g. Genus level) make this very powerful method
What is the best approach to identify regulator motifs? genome-wide ChIP analysis
What happens if "genome-wide ChIP analysis" is not available? 1) Known consensus sequence / PSSM generated using a limited data set 2) Microarray data indicating co-expressed genes (transcriptome analysis)
What are the benefits of a string search? Can include mismatches and IUPAC symbols Can quickly identify close matches NOT good for degenerate motifs
What is a 'string search'? Query is a string of nucleotides derived from consensus e.g. GTGnnnnCAC
PSSM-based search Query is a matrix-based pattern Weighted nature increases sensitivity Can identify degenerate motifs Trade-off between sensitivity and specificity
What web based tools can be used for motif discovery and searching?

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