129_Lecture5_2014

B and wunsch cd 1970 a general method applicable to

Info iconThis preview shows page 1. Sign up to view the full content.

View Full Document Right Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: equence Multiple sequence alignment: using conserved domains Sequences often contain highly conserved regions These regions can be used for an initial alignment How to generate a multiple sequence alignment? Raw Human Chimp Gorilla Orangutan Alignment NYLS NKYLS NFS NFLS 24 1/28/14 How to generate a multiple sequence alignment? Sequence elements are not truly independent but related by phylogeny: NYLS Raw Human Chimp Gorilla Orangutan Alignment NKYLS NFS NFLS Human Chimp Gorilla Orangutan NYLS NKYLS NFS NFLS How to generate a multiple sequence alignment? Sequence elements are not truly independent but related by phylogeny: NYLS Raw Human Chimp Gorilla Orangutan Alignment NKYLS NFS NFLS Human Chimp Gorilla Orangutan NYLS NKYLS NFS NFLS NF–S NFLS N–YLS NKYLS How to generate a multiple sequence alignment? Sequence elements are not truly independent but related by phylogeny: NYLS Raw Human Chimp Gorilla Orangutan Alignment NYLS N–YLS N KYLSN KYLS NFS N–F–S NFLS N–FLS NKYLS NFS NFLS Human Chimp Gorilla Orangutan N–YLS NKYLS NF–S NFLS 25 1/28/14 Multiple sequence alignment: Progressive method A) Perform pairwise alignments Multiple sequence alignment: Progressive method A) Perform pairwise alignments B) Cluster based on similarity Multiple sequence alignment: Progressive method B) Cluster based on similarity C) Generate Multiple Sequence Alignment A) Perform pairwise alignments 26 1/28/14 Some References on Alignments Global Alignment: Needleman, S.B. and Wunsch, C.D. (1970). "A general method applicable to the search for similarities in the amino acid sequence of two proteins". Journal of Molecular Biology 48 (3): 443–53 Local alignment: Smith, T.F. and Waterman, M.S. (1981) “Identification of Common Molecular Subsequences”. Journal of Molecular Biology 147: 195–197 ClustalW: Thompson, J. D., Higgins, D.G. and Gibson, T.J. (1994) “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice”. Nucleic Acids Research, 22:4673-4680 What have we learnt? 1)  Sequence analysis is one of the keys that will help us unravel the information coming from Genomics 2)  Vocabulary Analogy: The similarity of characteristics between two species that are not closely related Homology: Similarity in characteris<cs resul<ng from shared ancestry •  Paralog: Homologous sequences are paralogous if they were separated by a gene duplica<on event •  Ortholog: Homologous sequences are orthologous if they were separated by a specia<on event 3)  In bioinformatics we often assume that sequence similarity implies homology. However we do need to be cautious. What have we learnt? 4)  Sequence analysis starts with an analysis of its content 1)  DNAs: Charga...
View Full Document

Ask a homework question - tutors are online