Bioinformatics Flashcards
What are the problems with using BLAST to make metabolic networks?
Similar enzymes with close EC numbers but different functions have different functions
Holes/incomplete networks
Paralogs have same sequence but different function in different organisms
How is BLAST used to make metabolic networks?
Annotation of gene function based on alignment to existing sequences
Mapped onto KEGG reference network
Which proteins can be aligned by BLAST for networks?
Core metabolic processes only
not regulation or signalling
How can reliability of BLAST be improved?
Bidirectional BLAST
How can distant homologs be detected?
PSI/iterative searches
Hidden Markov Models
What proportion of distant homologs are detected by PSI BLAST?
40%
What results do Hidden Markov Models give?
Probability of relationship
How does BLAST work?
Gives probability sequences have a similarity caused by relationship not S=chance
E values show closeness of relationship
What does PRIAM do?
Annotates proteins based on EC number
When is PRIAM used?
SharkHunt software annotates raw genome sequence with introns/exons
metaTIGER database combines PRIAM alignments
What can metabolic networks be used for?
To find processes unique and essential to parasite that are absent in host/ will not cause large cascade implications
How many sequences are included in metaTIGER?
> 100 eukaryotes
>400 prokaryotes
What systems make quantitative studies of metabolic networks?
Biomolecular systems
Bipartitie graphs
Flux balance analysis
What structure do bimolecular systems have?
Protein vertices
Interaction edges
Can be labelled with names and strength of interaction
What are the disadvantages of bimolecular systems?
No direction of signal Impossible to represent stoichiometry Multiple cross links make it complicated Lots of unlinked edges Common substrates ignored
What is the structure of bipartite graphs?
2 sets of vertices for enzymes and metabolites
directional edges labelled with stiochiometry
What are matrixes?
A table version of bipartite graphs
What are the disadvantages of bipartite graphs?
No proton balancing
Complex lines from common substrates
When can Michaelis Menton kinetics be used to study flux?
In small systems such as single reactions
What data is needed for Michaelis Menton studies?
Kinetic constants for all reactions
Concentrations of all metabolites
What size of system can flux balance analysis be used for?
> 1000 reactions
What are the conditions of flux balance analysis?
Steady states must be maintained to measure [outputs] to determine rates of interconversion
In complex networks, which pathway is favoured?
The one that promotes most growth
What can flux balance analysis be used for?
Assessment of drug targets
Metabolic engineering
Determining effects of varying nutrients
