Abstract Summary: Here we present the MSA-PAD application, a DNA multiple sequence alignment framework that uses PFAM protein domain information to align DNA sequences encoding either single or multiple protein domains. MSA-PAD has two alignment options: gene and genome mode. Availability and Implementation: MSA-PAD is available as a web application (https://recasgateway.ba.infn.it/) and as two Taverna workflows corresponding to two alignment modes (Gene mode: http://www.myexperiment.org/workflows/4549.html; Genome Mode: http://www.myexperiment.org/workflows/4551.html). Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

Abstract Grid technology and ICT‐based infrastructures play a crucial role in the development of transnational multi‐disciplinary collaborations and allow scientists to share a wide range of distributed computational resources, regardless of their geographical location, and address new global scientific challenges. Till now, the strict security policy requested in order to access distributed computing resources has been a limiting factor when trying to broaden the adoption of Grids by wide communities of users. There is a steep learning curve to climb before starting to gain some benefits from this new technology. Grid security is indeed based on the Public Key Infrastructure (PKI) of X.509 certificate although the procedure to get and manage those certificates is unfortunately not straightforward. A first step to make Grids more appealing for new users has recently been achieved with the adoption of robot certificates. In this paper, the solution proposed by the Italian National Institute of Nuclear Physics to go through the complexity of Grid security and allow bioinformaticians to perform large‐scale Bayesian Phylogenetic analyses on the Grid by means of a web portal enabled by a robot certificate is presented. Copyright © 2010 John Wiley & Sons, Ltd.

The increasing use of phylogeny in biological studies is limited by the need to make available more efficient tools for computing distances between trees. The geodesic tree distance-introduced by Billera, Holmes, and Vogtmann-combines both the tree topology and edge lengths into a single metric. Despite the conceptual simplicity of the geodesic tree distance, algorithms to compute it don't scale well to large, real-world phylogenetic trees composed of hundred or even thousand leaves. In this paper, we propose the geodesic distance as an effective tool for exploring the likelihood profile in the space of phylogenetic trees, and we give a cubic time algorithm, GeoHeuristic, in order to compute an approximation of the distance. We compare it with the GTP algorithm, which calculates the exact distance, and the cone path length, which is another approximation, showing that GeoHeuristic achieves a quite good trade-off between accuracy (relative error always lower than 0.0001) and efficiency. We also prove the equivalence among GeoHeuristic, cone path, and Robinson-Foulds distances when assuming branch lengths equal to unity and we show empirically that, under this restriction, these distances are almost always equal to the actual geodesic.

BACKGROUND: Grid technology is the computing model which allows users to share a wide pletora of distributed computational resources regardless of their geographical location. Up to now, the high security policy requested in order to access distributed computing resources has been a rather big limiting factor when trying to broaden the usage of Grids into a wide community of users. Grid security is indeed based on the Public Key Infrastructure (PKI) of X.509 certificates and the procedure to get and manage those certificates is unfortunately not straightforward. A first step to make Grids more appealing for new users has recently been achieved with the adoption of robot certificates. METHODS: Robot certificates have recently been introduced to perform automated tasks on Grids on behalf of users. They are extremely useful for instance to automate grid service monitoring, data processing production, distributed data collection systems. Basically these certificates can be used to identify a person responsible for an unattended service or process acting as client and/or server. Robot certificates can be installed on a smart card and used behind a portal by everyone interested in running the related applications in a Grid environment using a user-friendly graphic interface. In this work, the GENIUS Grid Portal, powered by EnginFrame, has been extended in order to support the new authentication based on the adoption of these robot certificates. RESULTS: The work carried out and reported in this manuscript is particularly relevant for all users who are not familiar with personal digital certificates and the technical aspects of the Grid Security Infrastructure (GSI). The valuable benefits introduced by robot certificates in e-Science can so be extended to users belonging to several scientific domains, providing an asset in raising Grid awareness to a wide number of potential users. CONCLUSION: The adoption of Grid portals extended with robot certificates, can really contribute to creating transparent access to computational resources of Grid Infrastructures, enhancing the spread of this new paradigm in researchers' working life to address new global scientific challenges. The evaluated solution can of course be extended to other portals, applications and scientific communities.

BACKGROUND: A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA species markers has been taken in account. Unfortunately, a serious difficulty in the PCR and bioinformatic surveys is due to the presence of mobile introns in almost all the fungal mitochondrial genes. The aim of this work is to verify the incidence of this phenomenon in Ascomycota, testing, at the same time, a new bioinformatic tool for extracting and managing sequence databases annotations, in order to identify the mitochondrial gene regions where introns are missing so as to propose them as species markers. METHODS: The general trend towards a large occurrence of introns in the mitochondrial genome of Fungi has been confirmed in Ascomycota by an extensive bioinformatic analysis, performed on all the entries concerning 11 mitochondrial protein coding genes and 2 mitochondrial rRNA (ribosomal RNA) specifying genes, belonging to this phylum, available in public nucleotide sequence databases. A new query approach has been developed to retrieve effectively introns information included in these entries. RESULTS: After comparing the new query-based approach with a blast-based procedure, with the aim of designing a faithful Ascomycota mitochondrial intron map, the first method appeared clearly the most accurate. Within this map, despite the large pervasiveness of introns, it is possible to distinguish specific regions comprised in several genes, including the full NADH dehydrogenase subunit 6 (ND6) gene, which could be considered as barcode candidates for Ascomycota due to their paucity of introns and to their length, above 400 bp, comparable to the lower end size of the length range of barcodes successfully used in animals. CONCLUSION: The development of the new query system described here would answer the pressing requirement to improve drastically the bioinformatics support to the DNA Barcode Initiative. The large scale investigation of Ascomycota mitochondrial introns performed through this tool, allowing to exclude the introns-rich sequences from the barcode candidates exploration, could be the first step towards a mitochondrial barcoding strategy for these organisms, similar to the standard approach employed in metazoans.

This works presents the porting on the grid of a parallel application of phylogenetic inference, MrBayes, in the LIBI (International Laboratory of Bioinformatics) platform. Moreover a bioinformatic case study about the analysis of 11 phylogenies, including a series of large sequences data sets that represent the nascent barcode reference database for Lepidoptera is also presented. The case study has been tested on the platform and the speedup and efficiency on Itanium HP XC6000 (Intel Itanium 2 processors and Quadrics interconnects) of the SPACI consortium, University of Salento, are described.