Machine Learning Meetup Notes: 2010-06-30: Difference between revisions
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Mike's bio overview: | |||
amino acids build proteins | amino acids build proteins | ||
20 amino acids | 20 amino acids | ||
protein has an amino acid sequence (three bases make up an amino acid) | *protein has an amino acid sequence (three bases make up an amino acid) | ||
dna comprised of 4 bases: A, T, C, G | *dna comprised of 4 bases: A, T, C, G | ||
rna comprised of 4 bases, A, U, C, G | *rna comprised of 4 bases, A, U, C, G | ||
*A goes with T | |||
*C with G | |||
every three bases is a codon, | |||
every three bases is a codon | |||
dave wrote a script that will take the codons and map them to their amino acids | dave wrote a script that will take the codons and map them to their amino acids | ||
protease - are a type of proteins that cleave other proteins? | *protease - are a type of proteins that cleave other proteins? | ||
*reverse transcriptase - takes viral rna and transcribes it into dna | |||
reverse transcriptase - takes viral rna and transcribes it into dna | *sends mrna (bad) into the ribosomes | ||
sends mrna (bad) into the ribosomes | *they replicate very fast in your immune cells and thats how they kill them | ||
they replicate very fast in your immune cells and thats how they kill them | |||
99 amino acids in protease (297 dna bases) | 99 amino acids in protease (297 dna bases) | ||
| Line 24: | Line 25: | ||
Possible Features: | Possible Features: | ||
*for the OR acids, perhaps create all possible combinations and weight them by 1/(number of combinations), normal rows weight = 1 | |||
*find most probable sequences (T) | |||
*correlating permutations (T) | |||
*molecular weight/length (E/Th) | |||
*acidity/charge | |||
*edit distance (differences between the sequences), use to cluster (A) | |||
*list of known resistant mvt sites (M) | |||
*find out which sites are most variable | |||
Liebenstein? | Liebenstein? | ||
for each site, and look at frequency of each amino acid | for each site, and look at frequency of each amino acid | ||
could put into a tree classifier | could put into a tree classifier | ||
Latest revision as of 22:21, 30 June 2010
Mike's bio overview:
amino acids build proteins
20 amino acids
- protein has an amino acid sequence (three bases make up an amino acid)
- dna comprised of 4 bases: A, T, C, G
- rna comprised of 4 bases, A, U, C, G
- A goes with T
- C with G
every three bases is a codon, dave wrote a script that will take the codons and map them to their amino acids
- protease - are a type of proteins that cleave other proteins?
- reverse transcriptase - takes viral rna and transcribes it into dna
- sends mrna (bad) into the ribosomes
- they replicate very fast in your immune cells and thats how they kill them
99 amino acids in protease (297 dna bases)
reverse transcriptase is not predictable - each sequence is a different length
Possible Features:
- for the OR acids, perhaps create all possible combinations and weight them by 1/(number of combinations), normal rows weight = 1
- find most probable sequences (T)
- correlating permutations (T)
- molecular weight/length (E/Th)
- acidity/charge
- edit distance (differences between the sequences), use to cluster (A)
- list of known resistant mvt sites (M)
- find out which sites are most variable
Liebenstein?
for each site, and look at frequency of each amino acid
could put into a tree classifier