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Sequence Alignment In Bioinformatics


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Sequence Alignment in Bioinformatics

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Sequence Alignment In Bioinformatics

  2. 2. Presentation Agenda <ul><li>What is sequence alignment & Why ? </li></ul><ul><li>Principles of sequence alignment </li></ul><ul><li>Sequence algorithms/tools </li></ul><ul><li>Problem statement </li></ul><ul><li>Objective of the study </li></ul><ul><li>Filaggrin gene mutation </li></ul><ul><li>Current status </li></ul><ul><li>How ? Proposed methodology </li></ul><ul><li>Scope & Limitations </li></ul><ul><li>Benefits of the project </li></ul><ul><li>Scope for further research </li></ul><ul><li>Conclusion </li></ul>
  3. 3. What ? Why ? <ul><li>Way of arranging the sequences of DNA, RNA or protein to identify regions of similarity . </li></ul><ul><li>Helps in inferring functional , Structural or evolutionary relationship between the sequence </li></ul><ul><li>Sequence alignment methods are used to find the best- matching sequences </li></ul>
  4. 4. DNA Sequencing (Genetic code) <ul><li>To determine the nucleotides sequence of DNA. </li></ul><ul><li>( Adenine, Thymine, cytosine, Guanine ) </li></ul><ul><li>Uses of sequencing </li></ul><ul><li>it can be used to find genes, segments of DNA that code for a specific protein or phenotype </li></ul><ul><li>If a region of DNA has been sequenced, it can be screened for characteristic features of genes. </li></ul>
  5. 5. Principles of Sequence <ul><li>Alignment </li></ul><ul><li>Alignment is the task of locating “equivalent” regions of two or more sequences to maximize their similarity </li></ul><ul><li>NI K ESH NARAYANAN (RED : Mismatches) </li></ul><ul><li>NI G ESH NARAYAN - - ( gaps ) </li></ul>
  6. 6. Principles of Sequence Alignment <ul><li>Alignment can reveal homology between sequences </li></ul><ul><li>Similarity is descriptive term that tells about the degree of match between the two sequences </li></ul><ul><li>Sequence similarity does not always imply a common function </li></ul><ul><li>Conserved function does not always imply similarity at the sequence level </li></ul><ul><li>Convergent evolution: sequences are highly similar, but are not homologous </li></ul>
  7. 7. Scoring Alignments: The Main Principles <ul><li>Alignments of related sequences is expected to give good scores compared with alignments of randomly chosen sequences </li></ul><ul><li>The correct alignment of two related sequences should ideally be the one that gives the best score </li></ul><ul><li>In practice, the correct alignment does not necessarily have the best score, since no “perfect” scoring scheme has been devised </li></ul>
  8. 8. Percent Identity as a Measure for Quantifying Sequence Similarity <ul><li>Identity is the number of identical bases or amino acids matched between two aligned sequences </li></ul><ul><li>Percent identity is obtained by dividing this number by the total length of the aligned sequences and multiplying by 100 </li></ul>
  9. 9. Types of Alignment <ul><li>Based on Completeness </li></ul><ul><li>Global </li></ul><ul><li>Local </li></ul><ul><li>Based on Numbers </li></ul><ul><li>Pair wise alignment </li></ul><ul><li>Multiple sequence Alignment </li></ul>
  10. 10. Methods & Algorithms <ul><li>Dot matrix Method </li></ul><ul><li>Dynamic programming </li></ul><ul><li>Progressive Methods : Clustal, TCoffee </li></ul><ul><li>Iterative Methods </li></ul><ul><li>Motive finding </li></ul><ul><li>FASTA </li></ul><ul><li>BLAST </li></ul>
  11. 11. Problem Statement <ul><li>Identifying of Filaggrin Gene Mutation through sequence Analysis and identical patterns for filaggrin proteins </li></ul>
  12. 12. Filaggrin <ul><li>Filaggrins are filament-associated proteins which bind to keratin fibers in epithelial cells. which is normally found in large quantities in the outermost layers of the skin. This protein is essential for skin barrier function, helping to form a protective layer at the surface of the skin that keeps water in and keeps foreign organisms out. </li></ul>
  13. 13. 2008;122: 689-93 Filaggrin
  14. 14. Clinical significance <ul><li>Individuals with truncation mutation in the gene coding for filaggrin are strongly predisposed to a severe form of dry skin, (ichthyosis vulgaris), and/or eczema. [1] </li></ul><ul><li>Another study showed that many people with ichthyosis vulgaris also have eczema. Further research then showed a link between ichthyosis vulgaris, eczema and asthma. </li></ul>
  15. 15. A t least in a subset of those with a sthma , the filaggrin gene defect may be the fundamental predisposing factor not only for the development of eczema but also asthma
  16. 16. Objectives of the study <ul><li>To detect faulty filaggrin gene which may cause Eczema & Asthma </li></ul><ul><li>To find out the identical human proteins which may have functional similarity with filaggrin </li></ul><ul><li>To find out same or identical proteins from other species which may be helpful in therapeutics </li></ul>
  17. 17. Current Status <ul><li>Many studies have proved that mutation in filaggrin gene will cause deficiency/absence of filaggrin protein which may lead to eczema, Asthma etc. </li></ul><ul><li>Researches are going on to find out Medication/Gene therapy </li></ul>
  18. 18. Scope of proposed study <ul><li>Sequence analysis of infected person’s gene with healty gene </li></ul><ul><li>Probable persons’ gene ( hereditary threat ) </li></ul><ul><li>Identical protein sequence </li></ul>
  19. 19. Methodology <ul><li>To identify filaggrin gene mutation </li></ul><ul><li>Pair wise alignment </li></ul>
  20. 20. Methodology contd . <ul><li>To find out identical protein sequence </li></ul><ul><ul><li>multiple sequence analysis </li></ul></ul><ul><ul><li>BLAST </li></ul></ul>
  21. 21. Limitations <ul><li>Practical difficulties in getting specimen.( not a funded project ) </li></ul>
  22. 22. Expected benefits <ul><li>Preventive measures for susceptible persons </li></ul><ul><li>therapeutic -Identify similar proteins which might have similar functions as that of filaggrin. </li></ul><ul><li>Plant & Animal proteins – Proteins identical with filaggrin in plants and animals can be utilized for protein supplements </li></ul>
  23. 23. Scope for further research <ul><li>Finding Gene Therapy methods for Asthma/Eczema patients </li></ul>
  24. 24. Conclusion <ul><li>Drugs or other treatments aimed at the filaggrin gene are still some years away but researches in this direction give hope to those with these distressing conditions. Hope this study will contribute for the right direction. </li></ul>