SpammerHellDontDelete at 05:21, 1 July 2010

2010-07-01T05:21:32Z

← Older revision		Revision as of 22:21, 30 June 2010
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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

	~~A goes with T~~		every three bases is a codon,
	~~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		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)
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	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		*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		*find most probable sequences (T)
	-correlating permutations		*correlating permutations (T)
	-molecular weight/length		*molecular weight/length (E/Th)
	-acidity/charge		*acidity/charge
	-edit distance (differences between the sequences), use to cluster		*edit distance (differences between the sequences), use to cluster (A)
	-list of known resistant mvt sites		*list of known resistant mvt sites (M)
	-find out which sites are most variable		*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

SpammerHellDontDelete: Created page with '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…'

2010-07-01T05:18:13Z

Created page with '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…'

New page

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
-correlating permutations
-molecular weight/length
-acidity/charge
-edit distance (differences between the sequences), use to cluster
-list of known resistant mvt sites
-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

Machine Learning Meetup Notes: 2010-06-30 - Revision history

SpammerHellDontDelete at 05:21, 1 July 2010

SpammerHellDontDelete: Created page with '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…'