Author Archives: Mike
PoGO paper accepted in BMC Bioinformatics
Our paper describing PoGO (Prediction of Gene Ontoloty terms) is now available on the BMC Bioinformatics web site: http://www.biomedcentral.com/1471-2105/11/215/abstract
Genome wide computational analysis of C. graminicola for secreted proteins (and other topics)
Thon, M.R. and Sukno, S.A .2010. Colletotrichum Workshop. 10th European Conference on Fungal Genetics. Leeuwenhorst, Holland. April 2010. (Oral presentation)
GO Slim Analysis
Controlled vocabularies such as the Gene Ontology enable you to compare large numbers of genes and find differences in gene content. In this exercise we will compare the gene content of two fungi. 1. Programs such as PoGO and BLAST2GO … Continue reading
Phylogenetic Analysis Tutorial
Tutorial 1: Comparing gene trees and species trees. Among three species of fungi in the Class Sordariomycetes, there are three possible species trees (including an outgroup). In this tutorial, we will construct three gene trees and compare them to the … Continue reading
PROSITE Patterns Tutorial
Note: before beginning these tutorials, import the file (hydrophobins.geneious) into Geneious. Tutorial 1. Finding proteins that match a pattern. 1. Proteins that are secreted through the Agrobacterium tumefaciens type IV secretion system are reported to have the C terminal consensus pattern … Continue reading
Gene Identification Tutorial
DNA Sequence for these tutorials: oryza.fasta a segment of genomic DNA from (Oryza sativa). 1. First, we will align ESTs to the genomic DNA with BLASTN. Open the link to the Oryza genomic DNA segment above and copy/paste it into Geneious. … Continue reading
Multiple Sequence Alignment Tutorial
Making and Evaluating Multiple Sequence Alignments BALiBASE is a database of manually edited multiple sequence alignments (MSAs) used to evaluate new multiple sequence alignment algorithms. In this exercise we will use MSAs from BALiBASE to evaluate the performance of several … Continue reading
Protected: Bioinformática y Genómica Computacional
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Diagnostic sensitivity and specificity of different methods used by two laboratories for the detection of Phytophthora ramorum on multiple natural hosts
Vettraino, A., Sukno, S., Vannini, A. and Garbelotto, M. 2010. Plant Pathology 59:289-300.
PoGO is now available!
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 … Continue reading