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SooryaKiran Bioinformatics


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Bioinformatics venture from the campus of University of Kerala

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SooryaKiran Bioinformatics

  1. 1.
  2. 2. About us Global Bioinformatics solution provider through novel, customized, cost effective insilico solutions. We focuses on customized Bioinformatics solutions and Bioinformatics services.
  3. 3. Our mission is to contribute to Life Science industry and research by providing quality IT solutions and services Mission
  4. 4. Key Products Biolets: A biological sequence generator which incorporates various probability distribution functions for generating random numbers which are then mapped into either nucleotides or amino acids as per user selection Biopad: An intelligent notepad for biological sequence analysis. It has features like ORF finder, Restriction Enzyme finder, CpG island predictor and Homologous sequence identifier
  5. 5. University Collaboration C-GREx, a tool for visualization and analysis of patterns in DNA, RNA and amino acid sequences was developed jointly with Centre for Bioinformatics, University of Kerala, with funding from Dept. of Biotechnology, Government of India.
  6. 6. Key Projects SNP Analysis Tools Sequence Analysis Workbench mtDNA Analysis Suite
  7. 7. Service Portfolio
  8. 8. TEAM skill set matrix Application Area in Bioinformatics Languages/OS Algorithm Design and Development C, C++, Perl, HTML, XML, JavaScript, Java, GWT, Ajax,  Perl, PHP, BioPHP  Windows/Linux Sequence Analysis and Genome Annotation CADD, Drug discovery by virtual screening, pharmacophore analysis and de novo approach, in silico ADMET analysis, Homology modeling. Database development, data mining  and data curation
  9. 9. Global Clients <ul><ul><ul><li>GSC, RIKEN , Yokahama, Japan </li></ul></ul></ul><ul><ul><ul><li>MITOCHONDRIA – mito research, Buffalo, USA </li></ul></ul></ul><ul><ul><ul><li>Argus Biosciences , California, USA </li></ul></ul></ul>
  10. 10. <ul><li>Services </li></ul>
  11. 11. <ul><li>Algorithm Design and Software Development </li></ul>
  12. 12. Algorithm Design and Software Development <ul><li>Development of high quality algorithms to solve complex Biological problems. </li></ul><ul><li>Customization of existing algorithms based on user requirement </li></ul><ul><li>Tailor made software tools in areas like genome analysis, structure prediction, phylogeny etc </li></ul><ul><li>Expertise in languages including C, C++, JAVA, GWT, PERL and PHP </li></ul>
  13. 13. <ul><li>Sequence Analysis </li></ul>
  14. 14. Sequence Analysis <ul><li>We offer annotation and functional interpretation of genomic data, elucidation of evolutionary relationships and user defined sequence analysis. </li></ul>
  15. 15. Sequence Analysis <ul><li>Sequence analysis includes the use of various bioinformatics methods to determine the biological function and/or structure of genes they code for. </li></ul><ul><li>Our Sequence analysis service is categorized into two </li></ul><ul><li> i) DNA sequence analysis ii) Protein sequence analysis </li></ul>
  16. 16. DNA sequence analysis <ul><li>Feature representation of physiochemical properties such as Molecular weight, GC content and evolutionary features. </li></ul><ul><li>Similarity Search– It finds very short segment pairs(“seeds”) between the query and the database sequence. </li></ul><ul><li>Multiple sequence alignment- to align the sequences in order to elucidate their relatedness as well as their evolutionary origin. </li></ul><ul><li>Identification of DNA patterns </li></ul>
  17. 17. DNA sequence analysis <ul><li>Prediction of possible reading frames, CpG islands </li></ul><ul><li>Analyzing the biased usage of codons </li></ul><ul><li>Detection of different repeats such as direct, tandem and inverted </li></ul><ul><li>Insertion of point mutation, Silent mutation, Non Sense mutation and frame shift mutation </li></ul><ul><li>Mapping of restriction enzymes with their position and number of occurrences </li></ul>
  18. 18. Protein Sequence analysis services <ul><li>Feature representation of physiochemical properties such as Molecular weight, Amino acid composition and Isoelectric point. </li></ul><ul><li>Similarity search and Multiple sequence alignment for evolutionary relationship. </li></ul><ul><li>Detection of repeats, motifs in the sequence. </li></ul><ul><li>Prediction of coding sequence of amino acid sequence with reference to its codon usage table. </li></ul><ul><li>Calculate Hydropathy values and graphical representation of amino acid sequence . </li></ul>
  19. 19. <ul><li>Structural Bioinformatics & Drug Discovery </li></ul>
  20. 20. Structural Bioinformatics & Drug Design <ul><li>Structural bioinformatics helps scientists analyze and predict the three dimensional (3D) structure of large biological molecules such as proteins and nucleic acids. </li></ul><ul><li>Correlation of molecular structural information with experimentally- determined structural and functional information to the understanding of the basis of the biological phenomenon. </li></ul>
  21. 21. Structural Bioinformatics & Drug Design <ul><li>Three-dimensional models of protein structures are key to a detailed understanding of the molecular basis of protein function. </li></ul><ul><li>Combining sequence with structure information provides invaluable insights for rational strategies to design experiments such as site-directed mutagenesis, studies of disease related mutations, protein engineering, analysis of ligand specificity, or structure-based drug design. </li></ul>
  22. 22. Protein structure modeling <ul><li>Advancements in biomedical research and drug discovery require many proteins to be characterized in terms of their structure and biochemical functions. </li></ul><ul><li>Although the cost and time to experimentally characterize such proteins is prohibitive, computational methods, based on amino acid sequence similarities (homology) between proteins, hold great promise in uncovering the structure and function of new proteins. </li></ul>
  23. 23. <ul><li>Protein structure modeling has several attributes: </li></ul><ul><li>i) Finds similarities between two structures and fragments of proteins. </li></ul><ul><li>ii) Allows identification and analysis of structural similarities of proteins that do not have significant amino acid sequence similarity. </li></ul><ul><li>iii) Allows clustering of similar fragments of structures, which can be used to identify sequence patterns which will represent local structural motifs in proteins. </li></ul>Protein structure modeling
  24. 24. Drug Designing <ul><li>Computational methods permeates all aspects of drug discovery and forms the core of structure-based drug design. </li></ul><ul><li>Use of complementary experimental and informatics techniques increase the chance of success in many stages of the discovery process. </li></ul><ul><li>Identification of novel targets and elucidation of their functions to the discovery and development of lead compounds with desired properties. </li></ul>
  25. 25. <ul><li>Drug designing is used to analyze the </li></ul><ul><li>i) target structures for possible binding/ active sites </li></ul><ul><li>ii) generate candidate molecules </li></ul><ul><li>iii) dock these molecules with the target </li></ul><ul><li>iv) optimize the molecules to improve binding characteristics </li></ul>Drug Designing
  26. 26. <ul><li>Customized Data Curation </li></ul>
  27. 27. CUSTOMIZED DATA CURATION <ul><li>Our customized data curation service offer the data the client need and allows them to free their time and spend it on what matters to them most. </li></ul>We curate all life science databases as well as literatures to meet client requirements.
  28. 28. <ul><li>We are focused to create reusable integrated knowledgebase in the wide area of life science </li></ul><ul><li>We collect data from various available scientific databases and journals. </li></ul><ul><li>We work closely with the clients to develop a project plan that will ensure high-quality, secure data that is perfectly aligned with the research goals and generates value for their needs. </li></ul>CUSTOMIZED DATA CURATION
  29. 29. What we do <ul><li>Identify up-to-date content relevant to specific focus area </li></ul><ul><li>Review the available information </li></ul><ul><li>Find and rank publications and patents </li></ul><ul><li>Extract data from abstracts or full text </li></ul><ul><li>Format data in the format of clients choice: XML, Excel, ... </li></ul><ul><li>Deliver data packages to schedule </li></ul>
  30. 30. A typical literature curation project would include: <ul><li>Develop search terms based on the needs </li></ul><ul><li>Identify and gather target journals </li></ul><ul><li>Create a data structure and curation policies </li></ul><ul><li>Identify references </li></ul><ul><li>Curate references </li></ul><ul><li>Export and delivery of results  </li></ul>
  31. 31. <ul><li>Core data content includes gene characterization and functions, phenotype and disease model descriptions, DNA and protein sequence data, polymorphisms, gene mapping data and comparative gene data. </li></ul>CUSTOMIZED DATA CURATION
  32. 32. <ul><li>Case Study of projects </li></ul>
  33. 33. Case Study 1. <ul><li>Online tools to find polymorphisms in a genome </li></ul><ul><li>mtDNA analysis tools </li></ul><ul><li>Maternal ancestry analysis </li></ul><ul><li>Application in forensic science, Pharmacogenetics and population studies </li></ul><ul><li>Insilico Biology, Citations in WIKIPEDIA </li></ul>
  34. 34. Solution Features <ul><li>The tool was developed to identify differences in DNA sequences between a reference mitochondrial genome and a set of test genomes. </li></ul><ul><li>takes one standard reference sequence and one or more test sequences as its input </li></ul><ul><li>identifies variations in a set of test DNA sequences with respect to a standard reference sequence </li></ul><ul><li>generates a list of substitutions, insertions and deletions for each test sequences, determined by the reference sequence </li></ul><ul><li>Polymorphisms are reported in the standard format for mitochondrial DNA research, i.e., reference base/position/alternate base: for example A263G. </li></ul>
  35. 35. Key Benefits to Customer <ul><li>The tool allows multiple sequences to be compared and contrasted even when small insertions and deletions are present , </li></ul><ul><li>Grouping of continuous deletions or insertions in the test sequence into a single entity for better output handling. </li></ul><ul><li>The time to process a single mitochondrial genome and to deliver the results online is approximately 120 seconds. </li></ul><ul><li>Free encyclopedias like Wikipedia and genealogical communities like RootsWeb list this tool as the sole tool to find single nucleotide polymorphisms of a DNA sequence due to its simplicity and unique features. </li></ul>
  36. 36. System-Overview
  37. 37. Case Study 2. <ul><li>Genome Designer </li></ul><ul><li>Sequence Analysis work bench </li></ul>Client: RIKEN, Japan
  38. 38. Solution Provided <ul><li>  A smart widget with comprehensive sequence analysis features </li></ul><ul><li>iPredictor, that predict potential interacting partners of user defined sequence from a backend database. </li></ul><ul><li>Implemented one-to-one and Monte Carlo methods for codon optimization. A new strategy developed is under review. </li></ul>
  39. 39. System -overview
  40. 40. System –overview cont’d
  41. 41. Case Study 3. <ul><li>A suite of mitochondrial genome analysis tools </li></ul><ul><li>Identify the haplogroup and map it in the world map </li></ul><ul><li>Finds functional significance of mutations and their disease associations </li></ul>
  42. 42. Solution Provided <ul><li>The custom tool accepts mtDNA sequences and aligns it with a user defined standard reference sequence. </li></ul><ul><li>Provides information on nucleotide change, position, type of mutations, amino acid change etc. </li></ul><ul><li>Indicates any known disease associations with a particular mutation. </li></ul><ul><li>Finds haplogroups based on mutations and their positions. Indicate the regions of prevalence in world map. Best prediction available. </li></ul>
  43. 43. System-Overview
  44. 44. THANK YOU REACH US SooryaKiran Bioinformatics (P) Ltd., T-TBI, Nila, Technopark, Thiruvananthapuram- 695 584 Keralam, India Ph: +91 471 4060948 [email_address]