Sequence Alignment Flashcards
Explain the different kinds of mutations, along with the terms synonymous and non-synonymous mutations
Point mutations is the replacement of one nucleotide for another. A synonymous point mutation changes the nucleotide in a codon, but results in the same amino acid as before. A non-synonymous mutation results in a different aa than before.
Insertions leads to the addition of a set of nucleotides.
Deletions remove a set of nucleotides.
A framshift mutation adds or removes a set of nucleotides that is nut a multiple of three.
Explain the concepts of homologous, orthologous, and paralogous genes
Homologous genes are genes in evolution with a common ancestor.
Ortologous genes are genes that have the same function as before, but in new species (evolution of species).
Paralogous genes are genes that have evolved to have a different function as before in the same species (evolution of the gene).
Explain the difference between local and global alignment
Local alignent seeks to finde the best alignment for a part of the gene, and extends in both directions to align the sequences based on this.
Global alignment seeks to find the best alignment of the whole sequence/genome.
Explain the concept of scoring matrices and their use in alignment and relatedness of genes.
Scoring matrices says something about the probability of differences between the sequences occuring by chance. The higher the probability, the more likely it is that the sequences are homologous.
Explain what multiple sequence alignment is
A set of sequences are aligned . Homologous residues are aligned in coloums across the sequence, thus illustrating homologous residues that may say something about conserved regions (evolutionary). They may represent conserved residues, motifs, or features of secondary structures.
Explain how multiple sequence alignment can result in guide/phylogenetic trees
A multiple sequence alignment (progressive) uses pairwise alignments of all proteins to create a distance matrix (relatedness of all the sequences). The sequences of least distance are clustered together. Another cluster is created from the next two sequences of least dissimilarity, so on and so forth untill all sequences are clustered together. During this process a guide tree is created to illustrate the distances between the different sequences.
What is the difference between a guide tree and a phylogenetic tree?
The guide tree is based on the distance matrix of pairwise alignments of all the sequences. The phylogenetic tree is constructed from the guide tree using a HMM to determine the closest related sequences.
