Changes
no edit summary
<p>Products of evolution retain similarities. The similarities appear at many levels- related people, recently diverged species, tissues within an organism containing related cell types but varying protein expression patterns, amino acid sequences and structures of proteins and DNA sequences. </p>
<p>To trace the course of evolution, we must quantitatively measure such similarities. There are many possible objects of such analysis-sequences of individual genes, full-genome sequences, sequences and structures of proteins , anatomical features, apatterns of development and any other phenotypic character one might choose. </p>
<p> </p>
<p><span style="color:#0000CD"><strong>Pattern matching - the basic tool of bioinformatics</strong></span></p>
<p>To measure similarity between two sequences, find their optimal alignment - the best matching up of the individual characters and produce a cumulative score of the similarites between the characters at each position. </p>
<p> </p>
<p>Sequence alignment</p>
<p>- Given two or more sequences, we wish to</p>
<p>1. Measure their similarity</p>
<p>2. Understand how the residues match up</p>
<p>3. Observe patterns of conservation and variability </p>
<p>4. infer evolutionary relationships. </p>
<p> </p>
<p>The dot plot is a simple picture that gives an overview of pairwise sequence similairity. </p>
<p>Dot plots and alignments </p>
<p>A dot plot shows perspicuously the quality and distribution of the pattern of similarity between two sequences. Each possible alignment of the two sequences corresponds to a path through the dotplot, from upper left to lower right.</p>
<p>Global alignment assigns correspondences to all residues in the sequences. If one sequence is shorter than the other, the difference in length must be made up by insertions/ deletions. </p>
<p>Local alignment is a pattern - matching technique for identifying a match for a short probe sequence within a much longer text. </p>
<p>A very important extension of pairwise sequence alignment is multiple sequence alignment, the mutal alignment of three or more sequences. </p>
<p> </p>
<p>Definining the optimum alignment</p>
<p>Hamming / transition / transversion / The BLOSUM matrices / gap weighting / </p>
<p>To define optimal alignment, we must assign scores for each possible substitution and corresponding scores for gap initiation and extension .</p>
<p> </p>
<p> </p>
<p>Approximate methods for quick screening of databases</p>
<p>Multiple sequence alignments and pattern detection. </p>
<p>Profile</p>
<p>hidden markov models </p>
<p>BLAST search different databases</p>
<p>- BLASTN / BLASTX ./ BLASTP / TBLASTN / TBLASTX </p>
<p>A multiple matching in 3D structures </p>
<p> </p>
<p>Pattern matching in three-dimensional structures</p>
<p>Extraction of the maximum common substructure induces an alignment of the sequences. This is called a structural alignment. </p>
<p>A srructural alignment is nevertheless an alignment = an assignment of residue-residue correspondences. Instead of assigning the correspondence by matching the chracters in two or more sequences, a structural alignment assigns the correspondence to residues that occupy similar positions in space, relative to the molecular framework. </p>
<p> </p>
<p><span style="color:#0000CD"><strong>E</strong></span><span style="color:#0000CD"><strong>volution of protein sequences, structures, and functions</strong></span></p>
<p>The effects of single-site mutations</p>
<p>- A sequence that so lacked robsutness that nay mutation would destroy it, could not exist. It could have no neighboring precursor and processes of evolution could never find its sequence. </p>
<p>Evolution of protein structure and function</p>
<p> </p>
<p><span style="color:#0000CD"><strong>Phylogeny</strong></span></p>
<p>A phylogenetic tree is a diagram showing ancestor- descendant relationships, that captures a pattern of similarities, in that individuals or species closely linked in the tree have high similarity. </p>
<p>Homology/ Similiarity/ similarity and dissimilarity / Clustering / Groupers / splitters/ Hierarchical clustering / classification / phylogeny/ </p>
<p> </p>
<p>Phylogenetic trees</p>
<p>Evolutionary tree // root </p>
<p>Clustering methods</p>
<p>Batesiian methods</p>
<p> </p>
<p>The idea of phylogeny is to observe different degrees of similarity among species or higher taxa, assume that the species are related by descent from a common ancestor and that higher degress of similarity correspond to closer relationships, and to try to capture the relationships in a tree diagram showing ancestor - descendant relationships such that species more closely related according to the tree do have higher degrees of similarity. </p>
<p> </p>
<p>Maximum parsimony and maximum likelihood. </p>
<p> </p>
<p><span style="color:#0000CD"><strong>Short-circuiting evolution : Genetic engineering</strong></span></p>
<p> </p>