sequence alignment in bioinformatics
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IDENTIFYING OF FILAGGRIN GENE MUTATION THROUGH SEQUENCE ANALYSIS
NIKESH.N
Sequence Alignment in
Bioinformatics
Presentation Agenda
• What is 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
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
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.
Principles of Sequence
Alignment Alignment is the task of locating
“equivalent” regions of two or more sequences to maximize their similarity
NIKESH NARAYANAN (RED : Mismatches)NIGESH NARAYAN- - ( gaps )
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
Scoring Alignments:The Main 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
Percent Identity as a Measure forQuantifying 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
Types of Alignment
Based on Completeness• Global• Local
Based on Numbers• Pair wise alignment
• Multiple sequence Alignment
Methods & Algorithms
Dot matrix MethodDynamic programmingProgressive Methods : Clustal, TCoffeeIterative MethodsMotive findingFASTABLAST
Problem Statement
Identifying of Filaggrin Gene Mutation through sequence Analysis and identical patterns for filaggrin proteins
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.
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.
At least in a subset of those with asthma, the filaggrin gene defect may be the fundamental predisposing factor not only for the deve
lopment of eczema but also asthma
Objectives of the study
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
Current Status
Many studies 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
Scope of proposed study
• Sequence analysis of infected person’s gene with healty gene
• Probable persons’ gene ( hereditary threat )
• Identical protein sequence
Expected benefits
Preventive measures 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
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