Abstract
Rapid increase in protein sequence information from genome sequencing projects demand the intervention of bioinformatics tools to recognize interesting gene-products and associated function. Often, multiple algorithms need to be employed to improve accuracy in predictions and several structure prediction algorithms are on the public domain. Here, we report the availability of an Integrated Web-server as a bioinformatics online package dedicated for in-silico analysis of protein sequence and structure data (IWS). IWS provides web interface to both in-house and widely accepted programs from major bioinformatics groups, organized as 10 different modules. IWS also provides interactive images for Analysis Work Flow, which will provide transparency to the user to carry out analysis by moving across modules seamlessly and to perform their predictions in a rapid manner.
Availability
IWS is available from the URL: http://caps.ncbs.res.in/iws.
Keywords: protein sequence, structure analysis
Background
Bioinformatics is now in a transition state - “from a data-centric science to knowledge based science”, analysis and extraction of relevant information from huge amount of data from various high-throughput experiments remains as the major challenge in bioinformatics. Rapid increase in data generation has left us with many genes and proteins as ‘unknown’ or ‘hypothetical’ ones. As it is impossible to validate all the sequence data by means of biochemical experiments for confirmation of the likely associations, bioinformatics approaches can play an important role as a filter for recognizing potential gene products that can represent new fold or a novel function. Computational approaches enable the recognition of putative gene products of a family and to rationally design mutation experiments. Along with rapid incoming data, the availability of various resources to analyze the data has also increased. IWS is a compilation of in-house databases, web servers and web interface for various programs related to protein sequence and structure analyses clustered as ten modules. IWS is an easy-to-use web server, which will enable the novice as well as the expert users to carry out protein sequence and structure analysis rapidly and easily.
Implementation
IWS provides various tools and database related to protein sequence and structure analysis classified into 10 different modules. Detailed information about the available modules, various tools, URL and its applications are given in Table 1 (supplementary material). IWS provides the tools and database under the following 10 different modules: Database and Servers, Sequence Retrieval and Search, Alignment, Sequence Analysis, Secondary Structure Prediction, Structure Analysis, Protein Modeling and Structure Validation, Sequence-Structure analysis, Phylogeny and Fold Recognition. Some of the major programs and databases available from IWS are PSI-BLAST [1], CASCADE PSI-BLAST [2], PHYLIP [3], SEQPLOT, JOY [4], MODIP [5], SCANMOT [6], MODELLER [7], HARMONY [8], PASS2 [9], DSDBASE [10] etc. More than 40 bioinformatics resources for protein sequence and structure analysis is available from IWS. Figure 1 illustrates a flowchart that explains about different databases and tools available from IWS. IWS is running on a CentOS-Apache server. Front-end of IWS is developed using HTML, Perl script, CGI script, and Java scripts. Back-end is a combination of different programs developed using different languages like FORTRAN, C library (GD), C++, and Perl.
Figure 1.
Schematic flow-chart about different databases and tools available from IWS
Input-output options
IWS accepts sequences in FASTA, PIR, and Phylip format for protein sequence analysis and PDB file format for structure analysis. IWS generates different output for different programs. For instance, we have projected the results of the run on an ‘unknown protein’ sequence (from Drosophila ambigua (gi: 3676414) from NCBI Protein database) at the URL: http://caps.ncbs.res.in/iws/unknown/example1.html.
Caveats and future directions
IWS can be accessible using any standard web-browsers (IE, Mozilla, Opera, Firefox etc.). We are planning to upgrade IWS version 2 as cluster-based server. We will continue to integrate new tools as they become available from the lab.
Conclusion
In this article, we have explained about the availability of a new web server, NCBS-IWS an integrated web server for protein sequence and structure analysis. IWS will be a useful resource for research and academic communities interested in protein sequence and structure analysis.
Supplementary materials
Acknowledgments
R.S. was a Senior Research Fellow of the Wellcome Trust; U.K. K.S. was briefly supported by the Wellcome Trust Grant. We thank Mr. G. Pugalenthi for useful discussions. We also thank NCBS (TIFR) for financial and infrastructural support.
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