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Software
Tools and Databases
Currently, we have implemented
and are running in our BioINFORMATICS server, the following
Web tools:
SNP
Identification Pipeline: reads trace data from a folder,
process the data by ‘PHRED’, generates fasta sequences,
PHD files, QUAL files. 'PHRAP' process the fasta sequences
and produces ‘.ACE’ file which is read by Polybayes
program. Results can be visualized using 'CONSED'.
W2H–EMBOSS
interface: W2H is a free WWW interface to sequence analysis
software tools like the GCG-Package (Genetic Computer Group
[now Accelrys]), <<the GCG apparently no longer exists—you
have to indicate this somehow>> EMBOSS (European Molecular
Biology Open [Source] Software Suite) or to derived services
(such as HUSAR, Heidelberg Unix Sequence Analysis Resources).
G-Pipe/PISE
interface: G-Pipe is a graphical pipeline generator that
allows the definition of pipelines, and parameterisation of
its component methods using Pise web interfaces. The entire
analysis protocol is stored in XML and a complete bioinformatic
experiment (linked set of methods and parameters) can hence
be reproduced or shared among users. "PISE" is a
tool to generate Web interfaces for Molecular Biology programs.
StackPACK™
v2.1: The stackPACK clustering system allows rapid clustering,
alignment and analysis of ESTs, as well as full-length sequences
by providing sophisticated gene indexing capabilities that
go well beyond other clustering and assembly tools.
Web for designing PC primer :
PCR
Primers Design Primer3PLUS: Primer3 is a widely used program
for designing PCR primers (PCR = "Polymerase Chain Reaction").
PCR is an essential and ubiquitous tool in genetics and molecular
biology.
Primer3 can also design hybridization probes and sequencing
primers. PCR is used for many different goals. Consequently,
Primer3 has many different input parameters that you control
and that tell primer3 exactly what characteristics make good
primers for your goals.
WebAGCol:
Phaseolus: The WebAGCoL package is a set of four tools:
WebFPC displays contigs in a view very similar to the FPC
display. WebChrom shows contigs and genetic markers aligned
to the chromosome. It also allows the user to view the distribution
of markers based on name or remark.
WebFCmp allows fingerprint comparisons of a user-selected
clone set against the entire FPC database. WebBSS locates
a user supplied sequence on an FPC map based on its similarity
to sequences associated with other clones in the map.
IPHIS:
CIAT ICIS5 Phaseolus: This Is the Phaseolus implementation
of the International Crop Information System (ICIS)
which is a database system that provides integrated management
of global information on genetic resources and crop cultivars.
This includes germplasm pedigrees, field evaluations, structural
and functional genomic data (including links to external plant
databases) and environmental (GIS) data.
Databases
BLAST ACCESS: Provides access to the main
NCBI databases locally hosted in our server, with a batch-processing
option.
Blast
at CIAT
Blast-Batch
at CIAT (generic and By Species Bank)
Blast
(Species Bank One Sequence at Time)
dbEST or Expressed Sequence Tags database—Manihot
esculenta (cassava): A division of NCBI's GenBank,
containing a database on cassava (Manihot esculenta);
search possible by EST, contig, factor, and library; a BLAST
service available against this database:
Manihot
esculenta ESTs (CIAT)
Manihot
esculenta a Contigs Search (CIAT)
EST
Annotation Tools (Genoma-EMBRAPA)
AceDB databases: Genotypic databases for beans and
cassava:
CIAT
AceDB Home
Cassavagenes
Beangenes
Ricegenes
Phenotypic databases: Access to phenotypic
databases for information about passports and characterization
of different crops; and information about the collections
in CIAT's Genetic Resources Unit.
Cassava
DB
Rice
DB
Forrages
DB
URG
DB
Crosses
of Rice
LIMS: Laboratory Information Management
System (LIMSYS). A software developed by a Local Software
Company (DataBio).
AXLIMS
V 1.0 (Demo Last version of LIMS; User:demo Pwd:demo)
LIMSYS
V3.0
Admon
of PostgreSQL
BASE: BioArray Software Environment. Database
for managing and analyzing data generated by microarray analyses.
BASE
2.4
Admon
of MySQL
MOLCAS: Access point to the Cassava Molecular
Diversity Network.
MOLCAS
MASCAS
Cassava
NCBI Map Viewer
Biotechnology
Information Online
 At
CIAT, we are conducting research on the central crops of the
national economy: cassava, beans, and rice. We have developed
molecular biology technologies that help improve the productivity
of these crops. The application of these technologies at different
levels such as DNA sequencing, mapping, and gene expression
analysis has generated a large amount of biological information.
Moreover, considerable information also exists at several
biological levels—phenotypic, genotypic, and physiological—that
needs to be linked. Such linkage can be achieved through computational
biology.
Currently, the available information generated by CIAT is
scattered through different operating systems, different hardware
platforms, and different programming languages. Furthermore,
online bioinformatics databases available to the public such
as Gramene, TAIR, AceDB, and those of the NCBI are heterogeneous
and not well known, and the platforms to work at a high throughput
level are not well implemented. Finally, the necessary tools
to store, manipulate, analyze, and share the information are
scarce or nonexistent. These inadequacies mean that, if the
information generated by CIAT is to be used efficiently and
be capable of in-depth analysis, then bioinformatics resources
must be developed and applied.
We are developing a Bioinformatics Platform to manipulate
and analyze a large amount of information. For now, we have
focused on a bioinformatics platform in sequence analysis,
but we expect that in the near future the platform will connect
all the sequence information with microarray analyses, SNPs
(single-nucleotide polymorphisms), and phenotypic and field
information.
Purpose
of the Site
To reach our goals, we are using software and specialized
tools, and designing and implementing databases.
This site is the launching point of many software tools and
the point of access to the different databases already established.
Thus, the site functions as a bioinformatics support for the
researcher.
Furthermore, the site links with other places related to
the area, or to collaborative projects in which CIAT is involved
(e.g., GCP and SINGER), or to other information relevant to
bioinformatics.
In this context, we are focusing on the development, adaptation,
and use of software tools to support genomics research. As
a multidisciplinary science, it involves biology, genetics,
computer science, and mathematics for analyzing and manipulating
sequences (DNA). The key challenge is to analyze the huge
number of sequences to understand and discover information
in terms of protein structures, functions, and evolution.
Contacts: Fernando
Rojas or Joe Tohme
CIAT Bioinformatics Platform
Biotechnology Research Unit
Centro Internacional de Agricultura Tropical (CIAT)
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