IGRANNOT: A Multiagent System for InterGenic Regions Annotation

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Title: IGRANNOT: A Multiagent System for InterGenic Regions Annotation

1
IGR-ANNOT A Multiagent System forInterGenic
Regions Annotation

2
Introduction

The exponential growth of genomic data has led to
an absolute requirement for computerized tools to
analyze this data.
A new genome sequencing does not answer all
questions about the organism. Progress is more
likely to come from comparing the genomes of
different organisms.

3
Introduction

There are many tools and techniques to compare
complete genomes and coding regions, but there is
a lack for techniques for compare non-coding
regions of DNA, which contains regulatory
elements.
Many of the differences between species may be
attributed to changes in the regulation of
transcription and translation.
Transcription and translation are often regulated
via elements that lie in intergenic regions.

4
InterGenic Regions

Intergenic regions are defined as the sequence
between the translational stop of a gene and
translational start of the next gene.
For obtaining intergenic regions of an organism
are necessary
the complete genome of this organism (the
nucleotides sequence)
the information about coding regions (start and
stop positions, orientation, and name).

5
InterGenic Regions

Our decision was to work with GenBank files
because they contain all this necessary
information for identifying coding regions, and
this information will be used to infer the
necessary information about intergenic regions.

6
InterGenic Regions

The format design is based on a tabular approach
and consists of the following items
Feature Key a single word or abbreviation
indicating functional group
Location instructions for finding a feature
Qualifiers auxiliary information about a
feature.

7
InterGenic Regions

An example of a feature in the feature table.
8
InterGenic Regions

InterGenic Regions naming conventions
IGR-O-G1-G2
where O FRBX depending on the previous and
next gene orientations,
and G1 and G2 are the names coding regions which
intergenic regions contains regulatory
information.

9
InterGenic Regions

Intergenic regions will be written in the GenBank
file format using the feature misc_feature.
According to the GenBank file format description,
this feature key is used for annotate regions of
biological interest which cannot be described by
any other feature key.

10
IGR-ANNOT Engineering Process

The multiagent approach is particularly
attractive to this problem because
information content is heterogeneous.
information can be distributed.
much of the annotation work for each gene can be
done by different laboratories using different
methodologies for annotate information about
genes.
We have used MASE and AgentTool to modelling the
agent.

11
IGR-ANNOT Engineering Process

12
IGR-ANNOT Engineering Process
13
IGR-ANNOT Engineering Process

To implementing this architecture, we have used
the Perl language, and it can be run on any
suitable platform.
Perl have many features, like string manipulation
facilities, that become it a very interesting
language to working with DNA sequences,
besides there are complete packages to
implementing multiagent systems.

14
Results Discussion

We have extensively used IGR-ANNOT to creating
intergenic regions annotation in several genomes
of Mycoplasmataceae family.
To getting a graphical view of annotation created
by our tool we have used the Artemis tool.
The next figures are presenting the Mycoplasma
Hyopneumoniae 232 genome.

15
Results Discussion
16
Results Discussion
17
Results Discussion
18
Results Discussion
19
Conclusions

This system is now successfully in use by
biologists at the UFRGS.
The result of IGR-ANNOT application provides an
easy way to comparing intergenic regions among
different organisms.
Although the positive results achieved until now
in genomes of Mycoplasmataceae family, further
tests will be performed, mainly using most
complexes genomes.

20
Future Works

Create an environment to InterGenic Regions
comparison.
IGR-ANNOT will be available publicly to other
biologists over the web at www.inf.ufrgs.br/scama
rgo in software section.

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