Scientists in ICRISAT’s Global Theme on Harnessing Biotechnology for the Poor employ a range of modern genomic technologies in their efforts to enhance the efficiency and effectiveness of crop improvement. A critical rate-limiting step in genomics is no longer data generation, but rather the speed at which data is captured, validated, analyzed and turned into useful knowledge.

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critical rate-limiting step in genomics is no longer data generation, but rather the speed at which data is
remove this rate-limiting step by providing the
software platforms for handling large volumes
of data. The Bioinformatics Unit focuses on
three key areas: (a) the development of an
appropriate platform for storage and retrieval of
for handling and validating the large volumes
of data with special emphasis on data quality;
and (c) the development of high-throughput
sequence analysis tools and methodologies
molecular markers, and as aids to annotation or
comparative genomics.
All the software development work has been
driven by the need to have software packages
that do not have operating system or hardware
dependencies. Today, the ideal computer
languages that implement this approach are
Perl or Java, each with their advantages in
terms of applications. Database development has largely been in Java, while Perl with its excellent text
are called “software pipelines”.
The impacts of the Bioinformatics Unit can be demonstrated by these examples of its activities:
• Information management systems: The Unit has developed a Laboratory Information Management
System (LIMS) that meets the needs of a moderately high-throughput molecular genotyping facility. LIMS
sorghum and millet. The application is also being tested for use at the French public institute, CIRAD, and
the Brazilian national program, EMBRAPA. The Bioinformatics Unit at CIMMYT – a sister CGIAR center
• Data validation and quality:
of errors being introduced at various levels of data generation, entry and manipulation. The LIMS helps
to reduce these at the data capture point by validating data entry, checking for inconsistencies and
possible. A critical next step is often some form of data manipulation. For SSR genotyping using modern
DNA sequencers, the manipulation step is to turn a “raw” allele size into its “actual” size – thus allowing
more accurate comparisons between varieties to be made. Algorithms that provide a strong statistical
basis for these “allele calls” have been implemented into a software package “Allelobin”. The package
is available both within the LIMS package, and as a standalone application – ensuring the highest data
quality for analysis. Allelobin has been widely distributed at workshops and is being used by scientists
Turning Data into Knowledge – The Impacts of Bioinformatics

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at CIRAD, IPGRI and Kasetsart University in
Thailand.
• Sequence analysis tools: When scientists
deal with a single DNA sequence or even a
few sequences, the desired analyses such
as motif searching and primer design are
relatively straightforward. It is when dealing
with several thousands of sequences, that
bioinformatics begins to have an impact. One
analysis into single components and identify
of the entire process. This may be through
building pipelines of software or implementing
applications in parallel. Some examples
include pipelines of open source software
used for putative functional annotation from
sequence homology, and parallelized versions
of open source multiple alignment and
assembly and parsing software, all of which are available as freeware. These tools are now being used
extensively by students and scientists at ICRISAT and many other local and international institutes. All
have been shared with potential users (eg, CIAT). Parallelized versions implemented on Linux clusters
with easy-to-use interfaces have excited interest amongst external users at CIP and CIMMYT.
• Strengthening capacity through collaborations: Over the past few years, there has been increased
During the last two years, ten graduate students have been accommodated in training programs each
year. These students are working towards
a degree in biotechnology or bioinformatics
and the programs provide them with hands-
on training opportunities. In-house capacity
is also strengthened through working with
collaborators from Central Institutes like
the Centre for DNA Fingerprinting and
Diagnostics, and the International Institute
of Information Technology, both located in
Hyderabad.
• New linkages with the corporate
sector: ICRISAT cannot do it alone. We
often seek out consultants and third-parties
that can provide the required expertise in
bioinformatics. One such company is the
Tata Consultancy Services (TCS), a leading
global information technology consulting,
services and business process outsourcing
organization. The Bioinformatics Unit has
been working with scientists of the Advanced Technology Centre, the R&D wing for bioinformatics at
TCS, to build partnerships in the areas of software platform development, high-throughput comparative
biology and systems biology.