Clustal W - Multiple Sequence alignment
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KEGG GenomeNet - Introduction ClustalW - Introduction - Algorithm - Flowchart Multiple Alignment Method - Introduction ClustalW – Work process
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Clustal W - Multiple Sequence alignment
- 1. ClustalW Rohith BH 1OX18BT031(Student) The Department of Biotechnology The Oxford College of Engineering Bangalore
- 2. Jens Martensson Content • KEGG GenomeNet - Introduction • ClustalW - Introduction - Algorithm - Flowchart • Multiple Alignment Method - Introduction • ClustalW – Work process • Introduction to other Similar Tools – ClusterΩ / Jalview • Live demonstration 2
- 3. Jens Martensson KEGG - GenomeNet • KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. • KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolom ics and other omics studies, modeling and simulation in systems biology, and translational research in drug development. • GenomeNet is one to the Bioinformatics database with tools 3
- 4. Jens Martensson ClustalW • ClustalW like the other Clustal tools is used for aligning multiple nucleotide or protein sequences in an efficient manner. • It uses progressive alignment methods- align the most similar sequences first and work their way down to the least similar sequences until a global alignment is created. • ClustalW is a matrix-based algorithm- tools like T Coffee and Dialign are consistency-based. ClustalW is fairly efficient algorithm competes - against other software. • This program requires three or more sequences in order to calculate a global alignment and for pairwise sequence alignment 4
- 5. Jens Martensson 5 Algorithm • ClustalW uses progressive alignment methods. sequences with the best alignment score are aligned first, then progressively more distant groups of sequences are aligned. • This heuristic approach is necessary due to the time and memory demand of finding the global optimal solution. • The first step to the algorithm is computing a rough distance matrix between each pair of sequences, also known as pairwise sequence alignment. • The next step is a neighbor-joining method that usesmidpoint rooting to create an overall guide tree.
- 7. Jens Martensson 7 Multiple Alignment Method The steps are summarized as follows: • Compare all sequences pairwise. • Perform cluster analysis on the pairwise data to generate a hierarchy for alignment. This may be in the form of a binary tree or a simple ordering • Build the multiple alignment by first aligning the most similar pair of sequences, then the next most similar pair and so on. Once an alignment of two sequences has been made, then this is fixed. Thus for a set of sequences A, B, C, D having aligned A with C and B with D the alignment of A, B, C, D is obtained by comparing the alignments of A and C with that of B and D using averaged scores at each aligned position.
- 8. Jens Martensson 8 ClustalW For multiple alignment • ClustaW is a general purpose multiple alignment program for DNA or proteins. • ClustalW is produced by Julie D. Thompson, Toby Gibson of European Molecular Biology Laboratory, Germany and Desmond Higgins of European Bioinformatics Institute, Cambridge, UK. • ClustalW can create multiple alignments, manipulate existing alignments, do profile analysis and create phylogenetic trees. • Alignment can be done by 2 methods: slow/accurate fast/approximate
- 9. Jens Martensson 9 ClustalW - Input Output format Input sequences Scoring matrix Gap scoring
- 10. Jens Martensson 10 ClustalW - Input Download • Downloading Protein sequence in FASTA format
- 11. Jens Martensson 11 ClustalW - Input Sequences are Entered
- 12. Jens Martensson 12 ClustalW - Input Sequences for alignment https://textsaver.flap.tv/lists/4a27
- 13. Jens Martensson 13 ClustalW - Output Match strength in decreasing order
- 16. Similar tools Clustal Ω / Jalview
- 17. Resources • https://www.genome.jp/tools-bin/clustalw • https://www.uniprot.org/uniprot/P02769 • Bioinformatics Tools for Multiple Sequence Alignment < EMBL-EBI • https://en.wikipedia.org/wiki/KEGG • https://www.google.com