Fungal Bioinformatics and Genetics Research

Diagnostic sensitivity and specificity of different methods used by two laboratories for the detection of Phytophthora ramorum on multiple natural hosts

Serenella — Thu, 07 Jan 2010 09:54:59 +0000

Vettraino, A., Sukno, S., Vannini, A. and Garbelotto, M. 2010. (Plant Pathology, published online 28 Dec 2009)

Abstract

Five detection methods were comparatively tested on putative Phytophthora ramorum field samples from 41 wild plant species. The tested methods included two culture-based assays, a DAS-ELISA-based polyclonal assay, a nested PCR-based assay, and a TaqMan real-time PCR assay. Diagnostic values including sensitivity, specificity, positive predictive value and negative predictive value were calculated for each method. The effects of host species, seasonality and host location were analysed and compared between two laboratories. Significant effects of season, host species and laboratory were detected. It is concluded that a combination of either culturing and molecular diagnosis or of two molecular assays is the most promising approach to diagnose this pathogen. Based on the results of this and other studies, diagnosis should occur as much as possible during wet and warm periods favourable to the pathogen, and proficiency tests should be performed to compare results obtained with molecular approaches in different laboratories. Furthermore, length of time lapsed between sample collection and processing strongly affected the diagnostic sensitivity of culture-based methods, and therefore needs to be taken into account when comparing results from different laboratories.

PoGO is now available!

Mike — Fri, 04 Dec 2009 10:18:38 +0000

PoGO (Prediction of Gene Ontology) is now available on our website. PoGO can assign Gene Ontology terms to proteins and also displays related information about the proteins, including InterPro terms, blast hits, and structure predictions made by HHPred. We still have a few details to work on but the main features are working. If you find any problems, please let us know!

Welcome to our new Ph.D. student Gabriel Rech

Mike — Fri, 23 Oct 2009 06:05:48 +0000

Gabriel Rech has just moved from Salta, Argentina to join our group as a Ph.D. student. His thesis research will be in the area of fungal comparative genomics.

Oferta tesis doctorales bioinformatica/genetica de hongos

Mike — Thu, 17 Sep 2009 13:28:46 +0000

El grupo de Genética del CIALE (Centro Hispanoluso de Investigaciones Agrarias, http://ciale.usal.es) de la Universidad de Salamanca esta dispuesto a apoyar las posibles solicitudes de candidatos que desearan incorporarse para realizar tesis doctorales (Programas de Becas del Ministerio y la Junta de Castilla y León, próxima convocatoria octubre-noviembre). El grupo cuenta con modernas instalaciones inauguradas en 2008.

Las personas que estén interesadas pueden obtener mas información acerca de las actividades del grupo en nuestra pagina Web

http://bioinformatica.vil.usal.es/

Se requiere la licenciatura en Biología, Farmacia Bioquímica o ingeniería (agrónomos), Biotecnología y similares, con un buen expediente para poder participar en las solicitudes de becas. Por favor incluir calificaciones (expediente con nota media).

Fecha limite de presentación de candidaturas: 5 de octubre 2009

Interesados enviar su curriculo a Dr. Michael R. Thon mthon@usal.es y Dr. Serenella Sukno ssukno@usal.es

A Database of Fungal Protein Clusters for Comparative Genomics

Serenella — Thu, 22 Jan 2009 09:18:43 +0000

Jung, J., Yi, G., Sukno, S.A. and Thon, M.R. 25th Fungal Genetics Conference, Asilomar, CA, USA. March 17-22, 2009.

The Fungal Protein Cluster Database (FPC-DB) enables users to quickly locate information about the phylogeny and functional categories of fungal proteins and gene families and present the information in a number of comparative views. The proteins from fungal whole-genome sequencing projects are annotated with InterPro and Gene Ontology terms using an automated functional classification server previously developed in our group. The proteins are then clustered into putative gene families. Each protein cluster includes multiple sequence alignments, phylogenetic trees and a summary of functional categories found in the cluster. Users can perform queries using protein IDs, protein functional categories, and species names as search terms. The results are displayed in a variety of forms that allow users to compare the occurrence of gene and their functional categories between species. Users can also view a detailed page for each protein cluster and simultaneously view a phylogenetic tree and a matrix of functional categories. Comparative views enable users to directly compare gene family content between species to identify changes in gene family size between species.

A Protein Function Classifier for Fungi

Serenella — Thu, 22 Jan 2009 09:12:33 +0000

Jung, J., Yi, G., Sukno, S.A. and Thon, M.R. 25th Fungal Genetics Conference, Asilomar, CA, USA. March 17-22, 2009.

The Gene Ontology (GO) is a controlled vocabulary of terms to describe protein functions. It also includes a hierarchical description of the relationships among the terms in the form of a directed acyclic graph (DAG). Several systems have been developed that employ pattern recognition to assign gene function, using a variety of features, including sequence similarity, presence of protein functional domains and gene expression patterns, but most of these approaches have not considered the hierarchical structure of the GO. The DAG represents the functional relationships between the GO terms, thus it should be an important component of an automated annotation system. We have developed a Bayesian, multi-label classifier that incorporates the relationships among GO terms found in the GO DAG. We trained the classifier using more than 6000 annotated proteins from fungi obtained from public databases. A comparative analysis of our method to other previously described annotation systems shows that our method provides improved annotation accuracy. More importantly, our method enables the classification of significantly more GO terms to more proteins than other classifiers.

Protected: file upload

Mike — Wed, 10 Dec 2008 08:25:50 +0000

Protected: manuscrito de Davi

Mike — Tue, 25 Nov 2008 19:15:12 +0000

Protected: Phylogenetic Analysis Tutorial

Mike — Wed, 19 Nov 2008 15:14:57 +0000

Protected: Using PRATT and Hmmer to Model Multiple Sequence Alignments

Mike — Tue, 18 Nov 2008 16:49:47 +0000