October 6, 2009

Dinucleotide Properties Genome Browser: DiProGB

Filed under: Bioinformatics,Computational Biology — Biointelligence: Education,Training & Consultancy Services @ 6:08 am
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Whole genomes have now been sequenced from a long time. The basic aim of computational genome analysis is to understand the information encoded in the genomes. Apart from the nucleotide sequence, the related physical properties also play an important role.

DiProGB is a standalone computer program written in VC++.It is an easy to use new genome browser that encodes the primary nucleotide sequence by thermodynamical and geometrical dinucleotide properties. The nucleotide sequence is thus converted into a sequence graph. This visualization, supported by different graph manipulation options, facilitates genome analyses, because the human brain can process visual information better than textual information. Also, DiProGB can identify genomic regions where certain physical properties are more conserved than the nucleotide sequence itself.DiProGB adds a new dimension to the common genome analysis approaches by taking into account the physical properties of DNA and RNA.

In DiProGB all annotated features such as genes, exons, introns or repeat regions and the corresponding qualifiers such as gene name, product and function can be separately addressed and specifically colored. All or parts of the annotated information can be displayed for either a single strand or for both strands together. Overlapping features are visualized by stacked bars in the so-called feature graph below the sequence graph.

More about DiProGB can be read from here:

September 10, 2009

Have large Genomics Data: Genephony is the tool for you !!

Filed under: Bioinformatics,Computational Biology — Biointelligence: Education,Training & Consultancy Services @ 7:49 am
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Beacuse of the increase in genome wide analysis experiments and due to adoption of high throughput experimental technologies, a large amount of data is generated. It is quite a tedious task to manage this data.Integration, exploration, manipulation and interpretation of data and information therefore need to become as automated as possible, since their scale and breadth are, in general, beyond the limits of what individual researchers and the basic data management tools in normal use can handle.

Genephony, hosted by University of Florida,  is an online tool to assist in this data management. It is a tool for manipulation of large datasets of genomic information. It can be used as a browser for genomic data, as a high-throughput annotation tool, and as a knowledge discovery tool. It is designed to be easy to use, flexible and extensible. Its knowledge management engine provides fine-grained control over individual data elements, as well as efficient operations on large datasets.It can also be used to manage large datasets of genomic information, integrating them with existing knowledge repositories.

Click here to access Genephony: