Bioinformatic tools in Pheromone technology

1. ROLE OF
BIOINFORMATICS TOOLS
IN PHEROMONE
TECHNOLOGY
LS 1154,
M.THILAKAR,
4’th M.Sc. LIFE SCIENCES,
BHARATHIDASAN UNIVERSITY,
TIRUCHIRAPALLI..

2. BIOINFORMATICS - INTRODUCTION
BIOLOGY + INFORMATICS = BIOINFORMATICS.
Deals with Data of Biology with the aid of computers and their
programs.
The programs are specially designed for the purpose of Biological
data analysis.
Biomolecules like Protein, Nucleic acids are predominantly subjected
to analyses.
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3. BIOINFORMATICS TOOLS
Tools in the sense of Software packages.
Software packages are written as coding and are prepared as
executable files.
Already existing software are available through online.
Programs like C, C++, PERL, Python etc., are commonly used to
create these software packages.
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4. ABOUT UNIPROT
The mission of UniProt is to provide the scientific community with a
comprehensive, high quality and freely accessible resource of protein sequence
and functional information.
UniProt is comprised of four components, each optimized for different uses:
1) The UniProt Knowledgebase (UniProtKB) is the central access point for
extensive curated protein information, including function, classification, and
cross-reference.
It consists of two sections:
UniProtKB/Swiss-Prot which is manually annotated and is reviewed and
UniProtKB/TrEMBL which is automatically annotated and is not reviewed.
2) The UniProt Reference Clusters (UniRef) databases provide clustered sets
of sequences from the UniProtKB and selected UniProt Archive records to
obtain complete coverage of sequence space at several resolutions while hiding
redundant sequences.
3) The UniProt Archive (UniParc) is a comprehensive repository, used to keep
track of sequences and their identifiers.
4) The UniProt Metagenomic and Environmental Sequences (UniMES) database4/6/2015 4LS1154 - M.THILAKAR

5. WHY IS UNIPROTKB COMPOSED OF 2 SECTIONS,
UNIPROTKB/SWISS-
PROT AND UNIPROTKB/TREMBL?
UniProtKB/Swiss-Prot
Created in 1986.
Manually annotated and
non-redundant protein
sequence database.
Brings together the
experimental results,
computed features and
scientific conclusions.
UniProtKB/TrEMBL
Created in 1996.
Because of the increased dataflow
which is resulting from Human
Genome project.
Contains high quality computationally
analyzed data and are automatic
annotation with classification.
Unreviewed entries kept separated
form Swiss-Prot.
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6. UNIPROT – HOME PAGE http://www.uniprot.org
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7. SEARCHING ON UNIPROT (ADVANCED)
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8. RESULT PAGE -
COMPLETE
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9. RESULT PAGE – SELECTED ORGANISM :
MOUSE
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10. RESULTS ARE
DOWNLOADABLE
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11. ALIGNMENT
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12. ALIGNMENT - RESULT
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13. ALIGNMENT - TREE RESULT
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14. BLAST
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15. BLAST PAGE IN UNIPROT
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16. BLAST
BLAST RESULTS
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18. DDBJ – DNA DATA BANK OF
JAPAN
DDBJ provides freely available nucleotide sequence data and super
computer system (for support in the research activities in Life sciences).
DDBJ is accessing from NIG-J with endorsement of Japanese Ministry of
Education, Culture, Sports, Science and Technology.
DNA database Advisory committee (from outside of NIG) and INSDC are
supports and reviews the DDBJ activities.
Major activities of DDBJ Center are as follows.
Construction and operation of INSDC rules and regulations.
Providing nucleotide and amino acid sequence data that are related to
patent applications.
Management and operation of the NIG Supercomputer System.
Providing services to search and to analyze biological data.
Training course and publication.
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20. DDBJ HOME PAGE AT : http://ddbj.nig.ac.jp
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21. COLLABORATIONS
DDBJ is the member of INSDC (International Nucleotide Sequence Database
Collaboration).
DDBJ exchanges their data with EMBL at European Bioinformatics institute and
with Genbank at National center for Biotechnology Information on Daily basis.
Thus three databanks contains same data at any time.
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EMBL HOME PAGE AT : http://www.embl.org

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NCBI HOME PAGE AT : http://www.ncbi.nlm.nih.gov

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DDBJ SEARCH AND ANALYSIS PAGE AT : http://www.ddbj.nig.ac.jp/searches-e.html

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DDBJ – ARSA SEARCH

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DDBJ – GETENTRY SEARCH

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DDBJ – GETENTRY SEARCH – RESULT PAGE FOR #Y17566

28. DDBJ – DATA SUBMISSION
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DDBJ SEQUENCE SUBMISSION PAGE :
http://ddbj.nig.ac.jp/submission

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DDBJSEQUENCE
SUBMISSION

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DDBJSEQUENCE
SUBMISSION

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DDBJSEQUENCE
SUBMISSION

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DDBJSEQUENCE
SUBMISSION

38. KEGG - INTRODUCTION
KEGG (Kyoto Encyclopedia of Genes and Genomes).
It is a database resource that integrates Genomic, Chemical and Systemic
functional information's.
Manually creates a knowledge base for Bio-systemic function by capturing and
organizing Experimental knowledge in Computable forms.
Such as KEGG pathway maps, BRITE functional hierarchies and KEGG modules.
It is a computer representation of Biological system consisting of Molecular
Building blocks of Genes and Proteins (Genomic information) and Chemical
substances (Chemical information) that are integrated with the knowledge on
Molecular Wiring Diagrams of interactions, Reactions and Relation networks.
It also contains the Disease and Drug information to the biological system.
KEGG is widely used as reference knowledge base for integration of Larger
datasets generated by Genome sequencing and other High throughput
experiments.
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KEGG HOME PAGE AT :
http://www.genome.jp/kegg/

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SEARCHING IN KEGG

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SEARCH RESULTS IN KEGG

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SEARCH RESULTS IN KEGG

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KEGG SIGNALING PATHWAY IN YEAST

45. PYMOL
Open source, User sponsored, Molecular visualization system
created by Warren Lyfor DeLano and Commercialization initialized by
DeLano Scientific LLC (A private software company).
It is currently commercialized by Schrödinger, Inc.
PyMOL can produce High quality 3D images of small molecules and
biological macromolecules such as proteins.
According to the original author of PyMOL, almost ¼ of images of
proteins are published as identified.
Accessible at : http://pymol.org
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46. %
PYMOL HOME PAGE AT http://pymol.org
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47. PYMOL SOFTWARE INSTALLED ON THIS
WINDOWS
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50. REFERENCES
http://www.uniprot.org
http://www.insdc.org
http://www.ddbj.nig.ac.jp
http://www.genome.jp/kegg/kegg1.html
https://pymol.org
http://www.ncbi.nlm.nih.gov
http://www.embl.org
http://en.wikipedia.org/wiki/DNA_Data_Bank_of_Japan
KEGG databases for pathway prediction by Susumu Goto Presented at
COSBi Seminar, 2010.
Introduction to KEGG by Susumu Goto Presented at Systems biology and
Osmics cascade, 2008.
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