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![Clinical significance 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] Another study showed that many people with ichthyosis vulgaris also have eczema. Further research then showed a link between ichthyosis vulgaris, eczema and asthma.](https://image.slidesharecdn.com/sequencealignmentinbioinformatics-100204112518-phpapp02/85/Sequence-Alignment-In-Bioinformatics-14-320.jpg)
![Clinical significance 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] Another study showed that many people with ichthyosis vulgaris also have eczema. Further research then showed a link between ichthyosis vulgaris, eczema and asthma.](https://image.slidesharecdn.com/sequencealignmentinbioinformatics-100204112518-phpapp02/75/Sequence-Alignment-In-Bioinformatics-14-2048.jpg)
Uploaded byNikesh Narayanan
Sequence Alignment In Bioinformatics
This document discusses identifying mutations in the filaggrin gene through sequence analysis. The filaggrin gene codes for filaggrin proteins that are essential for skin barrier function. Mutations in this gene are linked to conditions like eczema and asthma. The study aims to detect faulty filaggrin genes, identify other human and non-human proteins with similar function to filaggrin, and find identical protein sequences to help develop therapeutic options. Sequence alignment methods like pairwise alignment and BLAST will be used to analyze filaggrin genes and identify similar protein sequences.
In this document
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Introduction to sequence alignment in bioinformatics; agenda outlining principles and objectives for filaggrin gene mutation study.
Definition and purpose of sequence alignment; principles of establishing equivalence among sequences.
Principles of scoring alignments, percent identity calculation, and types of alignment methods.
Investigation of filaggrin gene mutation; role of filaggrin protein in skin barrier function.
Clinical relevance of filaggrin mutations linked to dry skin, eczema, and asthma susceptibility.
Objectives include detecting gene faults for related diseases; overview of current research on filaggrin mutations.
Proposed methodology involving sequence analysis, pairwise and multiple alignments to identify mutations.
Challenges in specimen acquisition; potential preventive measures and therapeutic benefits from findings.
Exploration of gene therapy avenues and concluding thoughts on the research contributions towards treatment.
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Sequence Alignment In Bioinformatics
- 1. IDENTIFYING OF FILAGGRINGENE MUTATION THROUGH SEQUENCE ANALYSIS NIKESH.N Sequence Alignment in Bioinformatics
- 2. Presentation Agenda Whatis sequence alignment & Why ? Principles of sequence alignment Sequence algorithms/tools Problem statement Objective of the study Filaggrin gene mutation Current status How ? Proposed methodology Scope & Limitations Benefits of the project Scope for further research Conclusion
- 3. What ? Why? Way of arranging the sequences of DNA, RNA or protein to identify regions of similarity . Helps in inferring functional , Structural or evolutionary relationship between the sequence Sequence alignment methods are used to find the best- matching sequences
- 4. DNA Sequencing(Genetic code) To determine the nucleotides sequence of DNA. ( Adenine, Thymine, cytosine, Guanine ) Uses of sequencing it can be used to find genes, segments of DNA that code for a specific protein or phenotype If a region of DNA has been sequenced, it can be screened for characteristic features of genes.
- 5. Principles of SequenceAlignment Alignment is the task of locating “equivalent” regions of two or more sequences to maximize their similarity NI K ESH NARAYANAN (RED : Mismatches) NI G ESH NARAYAN - - ( gaps )
- 6. Principles of SequenceAlignment Alignment can reveal homology between sequences Similarity is descriptive term that tells about the degree of match between the two sequences Sequence similarity does not always imply a common function Conserved function does not always imply similarity at the sequence level Convergent evolution: sequences are highly similar, but are not homologous
- 7. Scoring Alignments: TheMain Principles Alignments of related sequences is expected to give good scores compared with alignments of randomly chosen sequences The correct alignment of two related sequences should ideally be the one that gives the best score In practice, the correct alignment does not necessarily have the best score, since no “perfect” scoring scheme has been devised
- 8. Percent Identity asa Measure for Quantifying Sequence Similarity Identity is the number of identical bases or amino acids matched between two aligned sequences Percent identity is obtained by dividing this number by the total length of the aligned sequences and multiplying by 100
- 9. Types of AlignmentBased on Completeness Global Local Based on Numbers Pair wise alignment Multiple sequence Alignment
- 10. Methods & AlgorithmsDot matrix Method Dynamic programming Progressive Methods : Clustal, TCoffee Iterative Methods Motive finding FASTA BLAST
- 11. Problem Statement Identifyingof Filaggrin Gene Mutation through sequence Analysis and identical patterns for filaggrin proteins
- 12. Filaggrin 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.
- 13.
- 14. Clinical significance Individualswith truncation mutation in the gene coding for filaggrin are strongly predisposed to a severe form of dry skin, (ichthyosis vulgaris), and/or eczema. [1] Another study showed that many people with ichthyosis vulgaris also have eczema. Further research then showed a link between ichthyosis vulgaris, eczema and asthma.
- 15. A t leastin 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. Objectives of thestudy To detect faulty filaggrin gene which may cause Eczema & Asthma To find out the identical human proteins which may have functional similarity with filaggrin To find out same or identical proteins from other species which may be helpful in therapeutics
- 17. Current Status Manystudies have proved that mutation in filaggrin gene will cause deficiency/absence of filaggrin protein which may lead to eczema, Asthma etc. Researches are going on to find out Medication/Gene therapy
- 18. Scope of proposedstudy Sequence analysis of infected person’s gene with healty gene Probable persons’ gene ( hereditary threat ) Identical protein sequence
- 19. Methodology To identifyfilaggrin gene mutation Pair wise alignment
- 20. Methodology contd. To find out identical protein sequence multiple sequence analysis BLAST
- 21. Limitations Practical difficultiesin getting specimen.( not a funded project )
- 22. Expected benefits Preventivemeasures for susceptible persons therapeutic -Identify similar proteins which might have similar functions as that of filaggrin. Plant & Animal proteins – Proteins identical with filaggrin in plants and animals can be utilized for protein supplements
- 23. Scope for furtherresearch Finding Gene Therapy methods for Asthma/Eczema patients
- 24. Conclusion Drugs orother 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.