Emmanuel Oluseyi Ogunniyi

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BB201 - Bioinformatics Project

• Emmanuel Oluseyi Ogunniyi

BSc Pharmacology
Student no OGU3752S
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Introduction

• Bioinformatics is the study of the basic
  structure of biological information and
  biological systems. It brings together systematic
  biological data handling (e.g.of genomes) with
  the analytic theory and practical tools of
  mathematics and computer science. Each member of
  the team was given the sequence of a fragment of
  DNA to determine its characteristics.

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Aim

• The aim of this project is to use
  bioinformatics databases to
• Identify the origin of the given DNA sequence.
• Determine the EC code, structure and function of
  the the enzyme that relates to the given DNA
  sequence.
• Obtain the potential protein transitional
  products of a given DNA sequence as well as a
  reference.

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Procedure

• Each member was given a DNA sequence, mine was
• tatgctcgtgctcttcaatcttctgctatt
• This sequence was run through various databases
  so as to obtain the various characteristics of
  the given sequence. The first database used was
  the Nucleic Acid Translator database. The results
  obtained from this database are displayed on the
  next slide.

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Nucleic Acid Translator

• This database was used to translate the
  unknown fragment of DNA and to identify the
  correct reading frame. The database performed a
  rapid identity search and produced the following
  translations
• YARALQSSAI Chosen translation
• MLVLFNLLL
• CSCSSIFCY
• NSRRLKSTSI
• IAED!RARA
• !QKIEEHEH

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Nucleic Acid Translator

• Out of the 6 translations, 2 translations had
  stop codons in them and these were denoted by !
  and were ignored. One was pasted into the Owl
  database search form, and returned exact matches
  to the peptide.
• The next procedure was to search the Owl
  database for the peptide products. The site can
  be reached by clicking the link above and
  clicking the owl link in the blue section at the
  top of the page.

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Owl Database

• The Owl database produced 2 matches
• ALF_TRYBB FRUCTOSE-BISPHOSPHATE ALDOLASE,
  GLYCOSOMAL (EC 4.1.2.13). -TRYPANOSOMA BRUCEI
  BRUCEI.
• A54500 FRUCTOSE-BISPHOSPHATE ALDOLASE (EC
  4.1.2.13) - TRYPANOSOMA BRUCEI.

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Owl Database

• Both matches were similar, they had the same
  EC code. The 2 matches were for the same enzyme
  FRUCTOSE-BISPHOSPHATE ALDOLASE.
• The EC code was then put into the NCBI Database.
  And yielded the following results.

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NCBI Database

• The NCBI Database displays the structure of
  the molecule that had the EC code that was
  entered. The structure can be obtained by
  clicking on the top link (1EX5), this displays
  the MMDB structure summary. The MMDB id and PDB
  id are displayed at the top of the next page
  displayed. Clicking on the PDB id takes you to
  the PDB database.
• The PDB Database also gave information about
  the gene and these are displayed on the next
  slide.

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PDB Database

• Title Fructose 1,6-Bisphosphate Aldolase From
  Rabbit Muscle. Name Fructose 1,6-Bisphosphate
  Aldolase
• Origin Trypanosoma brucei brucei.EC Number
  4.1.2.13. Classification Lyase.
• Polymer Chains A, B, C, D
• Reference MEDLINE86055739 NCBI, ExPASy,
  Israel, Japan PubMed2998772 Clayton C.E.
  "Structure and regulated expression of genes
  encoding fructose bisphosphate aldolase in
  Trypanosoma brucei." EMBO J. 42997-3003(1985).

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PDB Database

• On the PDB Database click on the view
  structure link, the page displays the 3D
  structure that matches the EC code provided. On
  the right is the structure I obtained. There is
  also a link to obtaining the skeleton structure
  (shown on next slide) of the molecule on this
  page.

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Skeleton structure of the enzyme and links.

• Links
• To view this presentation on the internet.
• PDB Database
• NDBI Database
• John Mottleys webpage, this contains links to
  all the databases.