Intro + Pairwise alignment
10 important questions on Intro + Pairwise alignment
If we want to find the function of a newly sequenced gene with a 'lazy approach' (only bioinformatics, no biological experiments), how would we do this?
- Find a set of protein sequences similar to the unknown sequence.
- Identify similarities and differences.
- For long protein sequences: first identify domains and then use corresponding subsequences.
Name 3 things we look at for reconstructing evolutionary and functional relationships.
- Based on sequence
- identity (simplest)
- similarity
- Homology (ultimate goal)
- Other information such as 3D structure
What did a study on 3D structure and protein evolution show?
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What is a frame shift mutation?
What is a DNA expression mutation?
What can you entounter when reconstructing "evolution" with sequences?
Name conditions for aligning sequences.
- Sequences should be related trough divergent evolution
- so they should be homologous
- and preferablly orthologous:
- paralogous sequences can become too distant for correct alignment (think of BAD)
- Analogous sequences should not be aligned!
- Sometimes a short functional motif can be detected.
What should an alignment scoring method do? How is alignment score defined.
- Produce reasonable alignments
- Must assign scores to:
- substitutions (match/mismatch)
- DNA
- Proteins
- Gap penalties
- linear
- affine
- concave
Alignment score is defined as the summed score of all alignment columns.
Explain the concept of combinatorial explosion and the solution we use.
- 1 gap in 1 seq: n+1 possibilities for alignment
- 2 gaps in 1 seq: (n + 1)n
- 3 gaps in 1 seq: (n + 1)n(n - 1)
- *check formula later
explodes!
Solution = dynamic programming:
- breaks up alignment problem in smaller subproblems, solve them iteratively.
- Alignment is simulated as a Markov process. All sequence positions are seen as independent and identically distributed.
- Chanches of sequence events are independent
- Therefore probabilities per aligned position are multiplied
- AA matrices contain log odds --> sum
Name 2 alternative alignment methods (so not global, semiglobal local).
- De Novo sequencing
- tracks overlap between millions of short seq reads coming from seq experiment. N is number of reads --> N ^2 overlap matches required.
- Reference based sequencing
- aligns short reads against reference genome
These algorithms are not based on evolutionary considerations per se, but match (near)identical fragments
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