Bioinformatics

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Bioinformatics

• Information science has been applied to biology
  to produce the field called Bioinformatics.
• ?1. creation and maintenance of databases of
  biological information (Nucleic acid sequences)
• 2. researchers can both access existing
  information and submit new entries is only the
  beginning.
• 3. analysis of sequence information.

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• Sequencing of large portions of the genomes of
  several species have been sequenced in full
  (bacterial genomes, simple eukaryotes (e.g.,
  Saccharomyces cerevisiae,
• or baker's yeast)
• The Human Genome Project, designed to sequence
  all 24 of the human chromosomes. On 26 June 2000,
  the completion of the draft sequence of the Human
  Genome saw the sciences of biology and medicine
  change forever.

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Definition of Bioinformatics

• bioinformatics describes any use of computers to
  handle biological information.
• a synonym for "computational molecular
  biology"---the use of computers to characterize
  the molecular components of living things.
• use computers to store, retrieve, analyze or
  predict the composition or the structure of
  biomolecules.

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Definition of Bioinformatics

• "Biomolecules" include your genetic
  material---nucleic acids---and the products of
  your genes proteins. These are the concerns of
  "classical" bioinformatics, dealing primarily
  with sequence analysis.

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Definition of Bioinformatics

• "The mathematical, statistical and computing
  methods that aim to solve biological problems
  using DNA and amino acid sequences and related
  information."
• (Defined by Fredj Tekaia at the Institut Pasteur
  offers this definition of bioinformatics)

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Definition of Bioinformatics

• "I do not think all biological computing is
  bioinformatics, e.g. mathematical modelling is
  not bioinformatics, even when connected with
  biology-related problems. In my opinion,
  bioinformatics has to do with management and the
  subsequent use of biological information,
  particular genetic information."
• (interesting opinion by Richard Durbin, Head of
  Informatics at the Wellcome Trust Sanger
  Institute)

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• "Biomedical Informatics is an emerging discipline
  that has been defined as the study, invention,
  and implementation of structures and algorithms
  to improve communication, understanding and
  management of medical information."

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most common bioinformatics technology

• the technology of databases These databases
  include both "public" repositories of gene data
  like GenBank or the Protein DataBank (the PDB),
  and private databases, like those used by
  research groups involved in gene mapping projects
  or those held by biotech companies.

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• Databases of existing sequencing data can be used
  to identify homologues of new molecules that have
  been amplified and sequenced in the lab. The
  property of sharing a common ancestor, homology,
  can be a very powerful indicator in
  bioinformatics

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• Bioinformatics is used in primer design.
• Primers are short sequences needed to make many
  copies of (amplify) a piece of DNA as used in PCR

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• Use Entrez-PubMed
• Make sure you are clear about your aim first. If
  you are looking for a sequence for a specific
  scientific purpose then you might be best to
  start with a relevant human-generated
  publication. For example, you have cloned a gene
  which is part of a well-characterised biochemical
  pathway and you want to find other sequences of
  the same functional gene product in other species
  (orthologues) Entrez PubMed is your friend.

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/????????

• DNA sequence (?????????????????) ??????????????
  ????????? ???? mRNA, exon, intron
• Amino acid sequence (??????????????) ?
  ?????????????????????????????????????????? eg.
  ?????????????????????????????????? microarray
• Enzyme metabolic pathway? ?????????????????????
  ???????? metabolic pathway ???????????????????

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• ???????????????? ??????????????????????????????
• genomics, proteomics, metabolomics
• ???????? ?????? primer ????????????????????
• ?????????????????????????????????????????

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• Computer science Biological data

Bioinformatics
analysis
organized
Sequence analysis Gene mapping Evolutionary
history
DNA/Protein database
??????????????? bioinformatics
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??????????????????????????? bioinformatics
DNA sequence file
Protein sequence file
Multiple Sequence Alignment
Multiple Sequence Alignment
Primer, Probe design
3D structure of DNA
Restriction map
Motif analysis
3D analysis
Hydrohilic profile
Phylogenetic analysis
Molecule Evolution
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most common bioinformatics programs

• Popular sequence databases
• GenBank, MBL
• sequence search programs ? BLAST sequence
  analysis programs, ? EMBOSS and Staden packages,
• structure prediction programs ? THREADER or PHD
• or molecular imaging/modelling programs ? RasMol
  and WHATIF.

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• GenBank gt www.ncbl.nlm.nih.gov
• EMBLgt www.ebi.ac.uk
• DDBJ gt www.ddb.nig.ac.jp
• ?????????????????? retrieve ???????
• ATLAS http//vms.mips.biochem.mpg.de/mips/progra
  ms/atlas.html
• SRS http//www.bic.nus.edu.sg/srs5

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??????????? bioinformatics

• ????????????????????????????
• ???????????????????????
• ???????????????????????????????????
• ????????????????????????????????????????
• ?????????????????????????????????????????????????
  ?????????????????????????????????????
  ?????????????????????????
• BCR-abl p53 (???????????????)

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??????????? bioinformatics

• ???????????????????? ???????? ????????????????????
  ????????????????????????? (human genome
  project ????????????? ? ?????????????????????????
  ??????/???????????????)
• ????????????????????????/??????
  ?????????????????????????????? STI-571
  ??????????????????? protein kinase
  ???????????????????????? translocation ?????
  BCR-Abl ????? CML ?????????????????
• ???????????????????????????????????????