Echobase: keeping pace with Escherichia coli in the postgenomic era' - PowerPoint PPT Presentation

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Echobase: keeping pace with Escherichia coli in the postgenomic era'

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Isolated in 1886 by Theodor von Escherich, from the intestines of children. Normal ... Echobase is a boutique' database for the E. coli research community. ... – PowerPoint PPT presentation

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Title: Echobase: keeping pace with Escherichia coli in the postgenomic era'


1
Echobase keeping pace with Escherichia coli in
the post-genomic era.
  • Gavin H. Thomas and Kai Chung
  • Dept. of Molecular Biology and Biotechnology,
  • University of Sheffield,
  • UK.

2
  • Escherichia coli a model organism
  • Isolated in 1886 by Theodor von Escherich, from
    the intestines of children. Normal habitat is the
    mammalian intestine.
  • Use was favoured as grows quickly in the
    laboratory, is non-pathogenic and can be easily
    isolated.
  • Easy to prepare active cell extracts for
    biochemical analysis.
  • Many genetic techniques pioneered
  • in E. coli.
  • Knowledge built on knowledge.

3
Once the understand the biology of E. coli we
will understand the biology of an
elephant Jacques Monod
  • Pre-genome studies
  • Most important metabolic process discovered
  • Over 2000 gene products characterised.
  • Detailed chromosomal map of the locations of
    these genes
  • Think we understand E. coli quite well.

4
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5
  • First bacterial genome sequencing project to be
    initiated in 1991.
  • Took 6 years as was pioneering attempt.

How big is the genome?
4,639,221 base pairs (4.6 Mb)
What is in this sequence?
87.8 protein encoding genes 0.8 stable
RNAs 0.7 non-coding repeats 11 for
regulatory and other functions
How many protein encoding genes?
4288 protein encoding genes
6
Functional assignment of these genes into a
classification scheme
38 of these have no known function
Of these, 20 represent completely new classes
of protein
7
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8
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9
  • Echobase
  • Written with Kai Chung and Kiril Bogdanov
  • Department of Computer Science,University of
    Sheffield, UK as Kais MSc project.
  • Methods
  • Wanted a relational database that can be
    queried over the WWW which will incorporate all
    the information in the catalogue and additional
    usability.
  • WWW interfaces were written in HTML and .jsps.
  • Used MySQL as the database software and Tomcat
    as server applet.

10
Most of the data is stored in the genes
table. User and other update information in
additional tables Postgenomic studies will form
new relatable tables as the project develops.
11
Database structure
Clear
Search
search
Results
Gene
Submit_search
Link_search
Clear
Input Form
Successful
input
Submit_input
Input
submission successful
(success)
Successful
Submit_input
Input
Download
submission not successful
download
(error)
Home page
Home
userFooter menu options
Submit_login
login incorrect
Login
_at_Administration
login
Submit_loginlogin ok
Modify
Successful
Submit_modify
submission successful
modify
Modify
(success)
Successful
Recent
Submit_modify
Modify
submission not successful
recent
(error)
12
Database structure (2)
Successful
Submit_pass
change
Change Password
passwords match
(success)
Return
Successful
Change
change
password
Submit_
pass
passwords do not match
(error)
Search
Search
Search
Link_search
Gene
Results
Submit_
search_1
Logged in curator
Clear
n
Administratio
Review
Submit_review
Successful
Review
Link_review
(success)
Review
Select
Successful
Review
Review
Delete record
(error)
Submit_review
input not ok
Amend
Successful
Submit_amend
input ok
Amend
Amend
(success)
Amend_
Successful
Link_amend
Amend
this
Amend
Submit_amend
(error)
input not ok
13
Database structure (3)
Successful
Submit_add
Add
input ok
(success)
Add
Successful
Add
Add
Submit_add
(error)
input not ok
Delete
Successful
Delete
Logged in curator
Submit_delete
(success)
input ok
Successful
Delete
Delete
Delete
(error)
Backup
Successful
backup ok
Backup
(success)
Backup
backup not ok
Successful
Backup
(error)
14
  • Conclusions
  • Echobase is a boutique database for the E. coli
    research community.
  • Functions to keep researchers abreast of new
    discoveries and to provide a repository for data
    from post-genomic studies which will provide
    clues to the functions of other uncharacterised
    genes.
  • The data within it is of high quality, better
    than the archival databases for previously
    uncharacterised genes.
  • Acknowledgements
  • University of Birmingham for WWW resources.
  • Kiril Bogdanov, Dept. Computer Science,
    University of Sheffield.
  • Echobase http//web.bham.ac.uk/bcm4ght6/genome.htm
    l
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