Applications of bioinformatics
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The document outlines the applications of bioinformatics at three levels: organizing biological data for research, developing tools for data analysis (such as FASTA and BLAST), and analyzing data to derive biological insights. It discusses various computational problems in genetics, genomics, proteomics, and the use of tools for sequence comparison, genome annotation, and drug discovery. Additionally, it emphasizes the integration of bioinformatics in fields such as pharmacogenomics and systems biology for enhanced understanding of biological processes.
Applications of bioinformatics
- 1. Bioinformatics Amandeep Singh Assistant Professor, Department of Biotechnology, GSSDGS Khalsa College, Patiala. Applications
- 2. Applications of Bioinformatics At 3 levels: 1. Basic level Used to organize biological data to help the researchers to access information. Biological data Database Information Retrieval
- 3. Retrieval of Biological data Experiments StructureSequence Function Sequence Database Genomic sequence Database Proteomic sequence Database Structural Database Functional Database DNA structural Database Protein structural Database Genomic functional Database Proteomic functional Database TAGCATGC
- 4. 2. Second level To develop tools and resources that helps to analyze data i.e. for data analysis. 2 Tools FASTA (FAST-ALL) BLAST (Basic Local Alignment Search Tool ) For Similarity searching For both DNA and Proteins For Similarity searching For both DNA and Proteins Better for similarity searching in closely matched or locally optimal sequences Better for similarity searching in less similar sequences
- 5. 3. Third level To use these tools to analyze the data and interpret the results in a biological meaningful manner. Biological data Global Analysis
- 6. Information Search and Retrieval PubMed PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. eTBLAST Application that is used to compare a query set of sentences with a database of other text to identify the text in the database that is most similar to the query. Paper 1 Paper 2 Abstract Abstract Compare
- 7. Genetics Related Applications There are three types of computational problems in genetics: 1. Analysis of single sequence to access similarities with known genes. 2. Identification of typical features such as binding sites or derive evolutionary relationships through phylogenetic trees. 3. Complete genome analysis to identify members of gene families, determination of the chromosomal location of the gene etc.
- 8. Sequence Comparison Tools: BLAST and FASTA Linkage Analysis • Involves analysis of large amount of data. • It is used to identify the chromosomal location of genes that is used for disease identification. • Tools: (http://linkage.Rockefeller.edu/).
- 9. Phylogenetic Analysis • Phylogenetic Analysis is also known as molecular taxonomy. • It uses the representation of evolutionary information in the form of phylogenetic trees. • Tool: PHYLIP • The Tree of Life (http://tolweb.org/tree/) is collaborative Internet project containing infomration about phylogeny and biodiversity.
- 10. Genomics It refers to mapping, sequencing and analysis of genomes. Structural Genomics Functional Genomics Linkage analysis Molecular cytogenetics Physical mapping EST sequencing Genome sequencing Genome organization Gene expression Forward genetics Reverse genetics Comparative genomics Proteomics Metabolomics
- 11. Microarrays The transcriptional profile of most genes within a genome can be analyzed using microarrays. Transcriptional Profile Gene expression Cell Type ArrayExpress is a public repository of microarray data.
- 12. Sequence Assembly Used to assemble large number of individual sequence reads. Tools: 1. Phred/Phrap/Consed Suite: used to do the assembly and finishing of shotgun sequencing information. 2. PolyPhred: used for comparison with fluorescent based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitution.
- 13. Genome Annotation Genome annotation is the process of identifying functional elements along the sequence of a genome. Tools: Genome Annotation Consortium: : It is a multi-institution collaboration to assist in the annotation and analysis of genome sequences by bioinformatics. Other tools: GRAIL, GRAILExp and Pipeline III Genie: It is a tool to locate genes and it uses Hidden Markov Models (HMMs). There are several tools available at http://www.softberry.com
- 14. Proteomics • It is the study of how genes affect a person’s response to drugs. • It combine pharmacology (the science of drugs) and genomics (the study of genes and their functions) to develop effective, safe medications and doses that will be tailored to a person’s genetic makeup. Pharmacogenomics • It is the study of proteomes (proteins expressed by genome). • It refers to all proteins produced by a species and it varies with time.
- 15. Drug discovery and Computer-aided Drug Design Drug Discovery: Analysis of binding sites in target proteins or identification of structural features common to active compounds. Computer-aided Drug Design Uses bioinformatics tools for drug discovery.
- 16. System Biology It is an integrated multi-disciplinary approach in which you study pathways and networks. Tool: NRCAM: General Computational tool, the virtual cell for modelling cellular processes. https://www.genecards.org/cgi-bin/carddisp.pl?gene=NRCAM