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Lecture 19

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Biology 1002B
Denis Maxwell

Lecture 19: Molecular Homology 1. Strategies for determining if features are homologous  Evolution and selection act on phenotype and not genotype  Gene sequences can change but not necessarily affect phenotype  National Center for Biotechnology Information gene database  Comparative genomics o Sequence genomes  genome annotation  protein prediction  align sequences  determine homology  Genome annotation o Ascribe biological function and meaning to sequence o Gene/protein prediction  Don’t sequence proteins anymore through purification and isolation o Regulatory elements or biological function through similarity searches o Automated algorithms  Protein coding gene prediction/deduction o Which of the 6 possible reading frames are the most probable  Compare with similar sequences o Infer structural and functional similarity  Sequence alignment o BLAST – local (common)  Looks for regions of very high similarity  Doesn’t force two sequences to align  Faster and stronger o CLUSTRAL – global  Start at beginning of protein coding sequence  Tries to align all similar bases by adding gaps to try to get them to align  Slower and weaker 2. Sequences detected by annotation programs to detect open reading frames (ORF)  Computers looks for the longest open reading frame  Largest amino acid sequence from start and stop codon 3. Characteristics that are, and are not, common between homologous genes  Homology means common ancestor and does not mean similar  May or may not be common o Identical nucleotide or amino acid sequence o Identical length of polypeptide o Same function  Chlamy and volvox nucleotide alignment of glsA gene o Query – what you send down (chlamy) o Subject – volvox (asymmetrical division gene) o Nucleotides sequences are only similar and not the same (10 differences)  Lots of polymorphism, mutation  Chlamy and volvox amino acid sequence o Compare different reading fram
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