ALIGMENT
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important functions ⇐ conservation
varibility
patterns 🔁
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most important with db query
phylogenetic analysis
evolutionary relationship 🏈⚽
correspondence
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proteins
structures(20/30% similar)
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degree of similarity 🏀⚽
searchs
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homology
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genes/proteins
similarity
degree of similarity(%)
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motive
set of characters (NAs or AAs)
contiguos or not
orthology
paralogy
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if
25% aligned AAs
75% aligned Nucleotidies
yes or no answare
hom. sequences used to interpret new sequence
members of families
proteins that are related
identity unknown sequencies
conserved through evolution(i.e. the most important reagions)
overlap during sequencies(long molecules e.g DNA)
grammars
previous knowledge on functions
homology preferred
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dot matrix
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Filtering background noise
noise high in NAs seq
readability of the graph
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window
stringency
e.g. s=7,w=11 \(\Rightarrow \) every 11 chars if at least are equals keep that part of the seq
about motive size
pairwise alignment
substitution matrix
Optimal alignment = max scoring function = min distance function
distance
Levenshtein
Hamming
c1 != c1 \(\Rightarrow\) +1
insertion, deletion, substitution
editing distance
symmetric
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BLOSSUM
PAM
Percent/Point Accepted Mutations
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AAs(1978)
Nucleotides(1991)
AAs(1992)
evolutionary mutations
explicit evolutionary model
construction
1572 accepted mutations
71 related groups of proteins with 85% similarity
from probability of changes in related proteins/genes
global
relative / segments of AAs
PAMn = (PAM1)^n
BLOSSUMn \( \rightarrow \) n = % of similarity of the sequences of the blocks used in each clusters
PAM250 most used
Blocks Substitution Matrices
block = highly conserved region without gaps
BLOSSUM62 standard
large n for evolutionary relationship close in time
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implicit evolutionary model
based on sequences primary structure
gaps
consecutive gaps likely to be related to the same mutation
recommended by ClustalW
DNA
AAs(BLOSSUM64)
g0 = 10
ge = 0.1*l
ge = 1*l
g0 = 11
minimize gaps(insertions/deletions)
maximize aligned symbols
minimize different symbols aligned