QUIZ: Identifying regulatory elements in bacterial genomes

What is does the sigma factor do in the 'Transcription cycle in bacteria'?

What is the consensus sequence?

Where do the sigma factors interact with the DNA?

Where do repressors and activators bind? (picture)

Where do repressors and activators bind?

Where do most searches for regulatory elements focus on?

How is transcription initiation controlled?

What does the E.coli transcriptional network look like?

What is a DOR?

What is a DOR (picture)?

Why are most DNA binding sites bipartite?

What do the bipartite DNA binding sites recognise?

What does the interaction between a DNA binding complex and a dyad sequence look like?

Do most sites match the consensus sequence?

How do you represent DNA motifs?

How do 'sequence patterns' work?

What is a disadvantage of sequence patterns?

How do you conduct a PSWM?

What is the IUPAC?

What is a DNA sequence motif?

How do you conduct a PSSM?

What do 'pseudocounts and background frequency of particular nucleotide in genome' solve?

What is the formula used to work out PSSM?

How do we identify regulatory motifs?

What do the approaches for 'identifying regulatory motifs' rely on?

When conducting an intra-genome search for dyads, what do we search for?

What are "intra-genome searches for dyads" limited to ?

For "Intra-genome searches for dyads" what does statistical significance depend on?

What happens following identification of groups of significant dyads?

What can a PSSM be used for within Intra-genome searches for dyads ?

What is an "Inter-genome comparison of - orthologues"?

What is the best approach to identify regulator motifs?

What happens if "genome-wide ChIP analysis" is not available?

What are the benefits of a string search?

What is a 'string search'?

PSSM-based search

What web based tools can be used for motif discovery and searching?