Multiple Alignment - Bioinformatics and Biological Computing

More documents

Recommendations

Info

NYLS NK/-YLS Progressive Methods NKYLS NFS NFLS NK/- F/YL/-S Ancestor seq NFL/-S Tips in choosing your sequences General considerations J Sequences taken directly from the database can contain irrelevant data, (e.g: multiple genes, fragments of different lengths). Check your sequences and use only the relevant parts of them for the alignment. J If you align your own sequences, edit them and remove the unrelated data before alignment. J Try to use sequences with more or less the same length for alignment. Tips in choosing your sequences General considerations For most uses of multiple alignments: – The more sequences to align the better. – Don’t include similar (>80%) sequences. – Sub-groups should be pre-aligned separately, and one member of each subgroup should be included in the final multiple alignment. What you need to know about multiple alignment programs • Almost all programs will align whatever sequences the user gives as input. • They will always return an alignment, even if the sequences are completely unrelated. The biology thinking should be done by you. • Most programs will insert gaps. However, if inserted they are there to stay. • You need to check how the program you use treats end gaps.
Global multiple alignments methods Clustalw http://npsa-pbil.ibcp.fr/cgi-bi n/npsa_automat.plpage=npsa_clustalw.html MSA (limited to a small number of sequences) http://www.ibc.wustl.edu//ibc/msa.html Iterative multiple alignments methods DIALIGN http://www.gsf.de/biodv/dialign.html MultAlign http://protein.toulouse.inra.fr/multalign.html PRALIGN http://mathbio.nimr.mrc.ac.uk/~jhering/pralign Local multiple alignments methods BLOCKS http://blocks.fhcrc.org/blocks/ HMMER http://hmmer.wustl.edu/ MEME http://meme.sdsc.edu/meme/website SAM http://www.cse.ucsc.edu/research/compbio/sam.html ClustalW- for multiple alignment • ClustalW is a global multiple alignment program for DNA or protein. • ClustalW was produced by Julie D. Thompson, Toby Gibson of EMBL, Germany and Desmond Higgins of EBI, Cambridge, UK. • ClustalW is cited: 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.
Page 1 and 2: Multiple sequence alignment Shifra
Page 3 and 4: Why do we need multiple alignments
Page 5: Multiple Alignment Steps to create
Page 9 and 10: Clustalw calculates the genetic dis
Page 11 and 12: ClustalX ClustalX ClustalX ClustalX
Page 13 and 14: PileUp for Multiple Alignment • P
Page 15: Example of PrettyBox Output Problem

Multiple Alignment - Bioinformatics and Biological Computing

Create successful ePaper yourself

Delete template?

Save as template?