CSB472-Final Exam

dynamic programming local alignment

create ways to analysis the genome, build on the genome

applies the techniques created by computational genomics

quantitative measure, can imply homology(primary way that bioinformatics infers relationships)

qualitatve statment about common descent

duplication b/c of a speciation event

duplicaiton b/c of duplication within an organism

related through a horizontal gene transfer event

describes the physical co-localization of genetic loci on the same chromosome within an individual or species

only masks for the seeding step

NT(query) to NT-->NT

NT(query) to NT -->AA

NT(query) to AA-->AA

AA(query) to NT-->AA

AA to AA-->AA

Expect Threshold-a parameter that describes the number of hits one can "expect" by chance when searching a data based of this size

local pairwise alignment

see lect 2

like a word hit, but for FAST

(p-value)/[number of this searched(BLAST significant) or number of genes analysed(microarays)]

log-odds score (for a given amino acid pair)

MSA scoring method

Global and Progressive MSA program

a good iterative MSA

how dialign diagonals are scored

branch on a phylogenic map

where phylogenic trees branch

operational taxonomical unit

the state of the most rescent common ancestor

mutations that occur in only one end point

independent evolution to same character from same ancestral state

independent evolution to same character from different ancestral state

reversion to the ancesteral state

Unweighted Pair Grouping Method using Averages, a Distance Based Phylogentic Method

Distance Based Phylogentic Method

pattern

UPGMA and neighbor-joining

max parsimony and max likilihood

purine to purine or pyrimidine to pyrimidine

purine < --> pyrimidine

max parsimony phylogenetic method, but with weighting on different substituation

equal freq and unequal Tn vs Tv

calculates distance from substitutions (equal freq and equal rate)

unequal freq and equal rates

unequal freq and unequal Tn vs Tv

unequal freq and six unequal rates

refers to the idea that different sites will have different substitution rates

re-sampled alignments (boot strapping)

a record in a relational database

fields or column in a relational database

flat-file or relational

structured query language, used to create or query databases

extensible markup languange. it is NOT a flat file format. explicit tagging but larger file size.

understandable by a human, less stable than an accession number

a unique code for a given entry, often arbitrary

provides stable reference sequences of all molec involve din the central dogma

cluster EST and mRNA seq aong with conding seq and annotated genomic DNA in subsets of related seq

protien motif database

protein motif database

a controlled vocabulary for describing a knowledge systmem

gene expression database

gene expression database

for searching across databases

The maximum length L such that 50% of all bases lie in contigs atleast L bases long. generally,the longer the better

number of species

database of the fingerprints of different protein families

the set of motifs common to a protein family. the motifs are unweighted

(sum the freq of a given animo acid in the entire allignemnt)* log2 (of the aminoacid at the specific position we are looking at)

, it is possible to create a statistical model of a protein family. AKA PSSMs

moves through a series of states and emits an output

a heuristic method used of HMMs

dynamic programin based heuristic approach to using HMMs

a large collection of multiple sequence alignments and hidden Markov models covering many common protein families

a large collections of HMMs that were created based on structural similarity

database that integrates a bunch of different info on protein(structural, motif, HMM ect...)

Information content. think about it as the number of binary question (yes/no) question you must ask to find out what is at a given position

using genomic techniques to analysis groups of microorganisms in thier natural enviroments

Looks at 3rd asymmetry in possition use

looks at NT usage biases in all three codon possitions A-DIF/T-DIF/ect..

compairs the codons in all three reading frame to a prot of average AA comp, but not codon biases

prok transcription initiation seq

log (ratio) vs log (intensity)

a measure of centrality for data-sets and populations. It agrees with the median for symmetric data-sets or populations.

specify the metadata required for microarray submitions (e.g. tissue type and age and source)

specify the metadata required for microarray submitions. more comprehensive that MIAME

the probability of at least one fase positive in all the tests

fractions of tests that were FPs given some cut off value used to judge significance

Significance analysis of microarrays

a way of analysis if there is enrichment in your gene set for a given catagory

an array with proteins bound to te slide

an array with sugar boud to the slide

High scoring segment pairs

cut off score used when determining the extended word list in BLAST

a factor that turns sequence score into a probability

a factor to account for the number of comparisions

P=1-e^-E

P(x,y|M)

used when making PAM, see lect 4