July 24, 2010

COMA server for protein distant homology search

Filed under: Bioinformatics — Biointelligence: Education,Training & Consultancy Services @ 8:07 am

Detection of distant homology is a widely used computational approach for studying protein evolution, structure and function. Here, we report a homology search web server based on sequence profile–profile comparison. The user may perform searches in one of several regularly updated profile databases using either a single sequence or a multiple sequence alignment as an input. The same profile databases can also be downloaded for local use. The capabilities of the server are illustrated with the identification of new members of the highly diverse PD-(D/E)XK nuclease superfamily.


March 31, 2010

QDD: a user-friendly program to select micro satellite markers and design primers from large sequencing projects

Filed under: Bioinformatics,Computational Biology,Systems Biology — Biointelligence: Education,Training & Consultancy Services @ 12:02 am
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QDD is an open access program providing a user-friendly tool for microsatellite detection and primer design from large sets of DNA sequences. The program is designed to deal with all steps of treatment of raw sequences obtained from pyrosequencing of enriched DNA libraries, but it is also applicable to data obtained through other sequencing methods, using FASTA files as input. The following tasks are completed by QDD: tag sorting, adapter/vector removal, elimination of redundant sequences, detection of possible genomic multicopies (duplicated loci or transposable elements), stringent selection of target microsatellites and customizable primer design. It can treat up to one million sequences of a few hundred base pairs in the tag-sorting step, and up to 50 000 sequences in a single input file for the steps involving estimation of sequence similarity.

Availability: QDD is freely available under the GPL licence for Windows and Linux from the following web site:

March 29, 2010

webMGR: an online tool for the multiple genome rearrangement problem

Filed under: Bioinformatics,Computational Biology,Systems Biology — Biointelligence: Education,Training & Consultancy Services @ 12:00 am
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The algorithm MGR enables the reconstruction of rearrangement phylogenies based on gene or synteny block order in multiple genomes. Although MGR has been successfully applied to study the evolution of different sets of species, its utilization has been hampered by the prohibitive running time for some applications. In the current work, we have designed new heuristics that significantly speed up the tool without compromising its accuracy. Moreover, we have developed a web server (webMGR) that includes elaborate web output to facilitate navigation through the results.

webMGR can be accessed via

March 27, 2010

MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences

Filed under: Bioinformatics — Biointelligence: Education,Training & Consultancy Services @ 12:00 am
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We have created a suite of Java-based software to better provide taxonomic assignments to DNA sequences. We anticipate that the program will be useful for protistologists, virologists, mycologists and other microbial ecologists. The program relies on NCBI utilities including the BLAST software and Taxonomy database and is easily manipulated at the command-line to specify a BLAST candidate’s query-coverage or percent identity requirements; other options include the ability to set minimal consensus requirements (%) for each of the eight major taxonomic ranks (Domain, Kingdom, Phylum, …) and whether to consider lower scoring candidates when the top-hit lacks taxonomic classification.


March 19, 2010

Pandora, a PAthway and Network DiscOveRy Approach based on common biological evidence

Filed under: Bioinformatics — Biointelligence: Education,Training & Consultancy Services @ 12:05 pm
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Many biological phenomena involve extensive interactions between many of the biological pathways present in cells. However, extraction of all the inherent biological pathways remains a major challenge in systems biology. With the advent of high-throughput functional genomic techniques, it is now possible to infer biological pathways and pathway organization in a systematic way by integrating disparate biological information.

Results: Here, we propose a novel integrated approach that uses network topology to predict biological pathways. We integrated four types of biological evidence (protein–protein interaction, genetic interaction, domain–domain interaction and semantic similarity of Gene Ontology terms) to generate a functionally associated network. This network was then used to develop a new pathway finding algorithm to predict biological pathways in yeast. Our approach discovered 195 biological pathways and 31 functionally redundant pathway pairs in yeast. By comparing our identified pathways to three public pathway databases (KEGG, BioCyc and Reactome), we observed that our approach achieves a maximum positive predictive value of 12.8% and improves on other predictive approaches. This study allows us to reconstruct biological pathways and delineates cellular machinery in a systematic view.

Availability: The method has been implemented in Perl and is available for downloading from It is distributed under the terms of GPL (