Please enable JavaScript.
Coggle requires JavaScript to display documents.
ALIGMENT - Coggle Diagram
ALIGMENT
correspondence
proteins
structures(20/30% similar)
...
...
important functions \(\Leftarrow \) conservation
varibility
patterns :repeat:
phylogenetic analysis
evolutionary relationship :football::soccer:
degree of similarity :basketball::soccer:
most important with db query
searchs
homology
orthology
paralogy
Top: An ancestral gene duplicates to produce two paralogs (Genes A and B). A speciation event produces orthologs in the two daughter species. Bottom: in a separate species, an unrelated gene has a similar function (Gene C) but has a separate evolutionary origin and so is an analog.
.svg)
genes/proteins
if
25% aligned AAs
75% aligned Nucleotidies
yes or no answare
hom. sequences used to interpret new sequence
similarity
degree of similarity(%)
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)
motive
set of characters (NAs or AAs)
contiguos or not
grammars
previous knowledge on functions
homology preferred
dot matrix
Filtering background noise
noise high in NAs seq
readability of the graph
window
e.g. s=7,w=11 \(\Rightarrow \) every 11 chars if at least are equals keep that part of the seq
about motive size
stringency
pairwise alignment
substitution matrix
symmetric
BLOSSUM
AAs(1992)
relative / segments of AAs
BLOSSUMn \( \rightarrow \) n = % of similarity of the sequences of the blocks used in each clusters
Blocks Substitution Matrices
block = highly conserved region without gaps
BLOSSUM62 standard
large n for evolutionary relationship close in time
implicit evolutionary model
based on sequences primary structure
PAM
Percent/Point Accepted Mutations
AAs(1978)
Nucleotides(1991)
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
PAMn = (PAM1)^n
PAM250 most used
Optimal alignment = max scoring function = min distance function
minimize gaps(insertions/deletions)
maximize aligned symbols
minimize different symbols aligned
distance
Levenshtein
insertion, deletion, substitution
editing distance
Hamming
c1 != c1 \(\Rightarrow\) +1
gaps
consecutive gaps likely to be related to the same mutation
recommended by ClustalW
DNA
g0 = 10
ge = 0.1*l
AAs(BLOSSUM64)
ge = 1*l
g0 = 11