Bioinformatics Toolkit Research Articles

HCG structure: A logical perspective

The three dimensional crystal structure of hCG has been publish by Wu et al., Lapthorn et al., and Lustbader et al. The problem is that the crystal is missing 50% of the hCG molecular weight. It is missing the 4 N-linked and the 4 O-linked oligosaccharides and β-subunit amino acid residues 113–145. Here we add back in these missing structures, and considering 11 reported consequences we predict the final structure of hCG, hyperglycosylated hCG, nicked hCG and hCG free β-subunit. The consequences of 11 report are considered. The missing structures are examined by 2 webware programs, Bioinformatics Toolkit (Max Planck Institute), and Bioinformatics and Computational Biology (IIT Delhi). Structures are proposed for hCG, hyperglycosylated hCG, nicked hCG and hCG free β-subunit, considering the charge effect that the 12 or 19 sialic acid residues may have, movement of α-subunit loop 2 and movement of β-subunit safety belt.: Nicking causes a major structural change to β-subunit loop 2.

GCView: the genomic context viewer for protein homology searches

Genomic neighborhood can provide important insights into evolution and function of a protein or gene. When looking at operons, changes in operon structure and composition can only be revealed by looking at the operon as a whole. To facilitate the analysis of the genomic context of a query in multiple organisms we have developed Genomic Context Viewer (GCView). GCView accepts results from one or multiple protein homology searches such as BLASTp as input. For each hit, the neighboring protein-coding genes are extracted, the regions of homology are labeled for each input and the results are presented as a clear, interactive graphical output. It is also possible to add more searches to iteratively refine the output. GCView groups outputs by the hits for different proteins. This allows for easy comparison of different operon compositions and structures. The tool is embedded in the framework of the Bioinformatics Toolkit of the Max-Planck Institute for Developmental Biology (MPI Toolkit). Job results from the homology search tools inside the MPI Toolkit can be forwarded to GCView and results can be subsequently analyzed by sequence analysis tools. Results are stored online, allowing for later reinspection. GCView is freely available at http://toolkit.tuebingen.mpg.de/gcview.

Insilico Methodolgy - Resistin Involved In Diabesity

In the present study, the role of several genes/proteins involved in the evolution of diabesity have been studied by several bioinformatics tools and software. Sequence and Phylogenetic Analysis was done using SDSC Biology workbench, a web based bioinformatics toolkit. Our bioinformatics analysis reports resistin gene as ominous link with diabesity. This bioinformatics study will be useful for future studies towards therapeutic inventions of diabesity. A multiple sequence alignment approach is used followed by construction of phylogenetic tree to compare the homology of functional proteins in one species and between other species. Sequences are analyzed to find mutations, evolutionary relationships, predicting structure, function and its abnormalities.

The MPI Bioinformatics Toolkit for protein sequence analysis

The MPI Bioinformatics Toolkit is an interactive web service which offers access to a great variety of public and in-house bioinformatics tools. They are grouped into different sections that support sequence searches, multiple alignment, secondary and tertiary structure prediction and classification. Several public tools are offered in customized versions that extend their functionality. For example, PSI-BLAST can be run against regularly updated standard databases, customized user databases or selectable sets of genomes. Another tool, Quick2D, integrates the results of various secondary structure, transmembrane and disorder prediction programs into one view. The Toolkit provides a friendly and intuitive user interface with an online help facility. As a key feature, various tools are interconnected so that the results of one tool can be forwarded to other tools. One could run PSI-BLAST, parse out a multiple alignment of selected hits and send the results to a cluster analysis tool. The Toolkit framework and the tools developed in-house will be packaged and freely available under the GNU Lesser General Public Licence (LGPL). The Toolkit can be accessed at .

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis.

We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein–structure prediction. Individual tools can be seamlessly chained into pipelines allowing the user to conveniently process complex workflows without the necessity to take care of any format conversions or tedious parsing of intermediate results. The toolkit is part of the Max-Planck Integrated Gene Analysis System (MIGenAS) of the Max Planck Society available at (click ‘Start Toolkit’).