Bioinformatics
The effect of simulated censored data on estimates of heritability of longevity in the Thoroughbred racing industry
Authors: Eleanor M. Burns, Richard M. Enns and Dorian J. Garrick
We examined the impact of censored data on estimates of heritability of longevity. Longevity, defined as the length of productive racing life of an individual, is influenced by many factors. A simulated data set, modelled on the Irish Thoroughbred industry, was used to estimate heritabilities of longevity. Several scenarios re.. Read More»
- Genet. Mol. Res. 5(1):
X-meeting - 1st International Conference of the AB3C
Authors: Sandro Jos�© de Souza
Biology has always been associated with test tubes, microscopes, Petri dishes, and fruit flies, but this conventional view has significantly changed in the last ten years. A typical biology laboratory today has computers, robots and other fancy equipment that together churn out a huge amount of data. A significant part of biol.. Read More»
- Genet. Mol. Res. 5(1):
New strategy to detect single nucleotide polymorphisms
Authors: Miguel Galves, Jos�© Augusto Amgarten Quitzau and Zanoni Dias
A great effort has been made to identify and map a large set of single nucleotide polymorphisms. The goal is to determine human DNA variants that contribute most significantly to population variation in each trait. Different algorithms and software packages, such as PolyBayes and PolyPhred, have been developed to address this .. Read More»
- Genet. Mol. Res. 5(1):
BayBoots: a model-free Bayesian tool to identify class markers from gene expression data
Authors: Ricardo Z.N. V�ªncio, Diogo F.C. Patr�£o, Cassio S. Baptista, Carlos A.B. Pereira and Bianca Zingales
One of the goals of gene expression experiments is the identification of differentially expressed genes among populations that could be used as markers. For this purpose, we implemented a modelfree Bayesian approach in a user-friendly and freely available web-based tool called BayBoots. In spite of a common misunderstanding th.. Read More»
- Genet. Mol. Res. 5(1):
Building multiple sequence alignments with a flavor of HSSP alignments
Authors: Roberto Hiroshi Higa, Sergio Aparecido Braga da Cruz, Paula Regina Kuser, Michel Eduardo Beleza Yamagishi, Renato Fileto, Stanley Robson de Medeiros Oliveira, Ivan Mazoni, Edgard Henrique dos Santos, Adauto Luiz Mancini and Goran Neshich
Homology-derived secondary structure of proteins (HSSP) is a well-known database of multiple sequence alignments (MSAs) which merges information of protein sequences and their threedimensional structures. It is available for all proteins whose structure is deposited in the PDB. It is also used by STING and JavaProtein Dossier .. Read More»
- Genet. Mol. Res. 5(1):
Gene Class Expression: analysis tool of Gene Ontology terms with gene expression data
Authors: Gislaine S.P. Pereira, Rodrigo M. Brand�£o, Silvana Giuliatti, Marco A. Zago and Wilson A. Silva Jr.
Serial analysis of gene expression (SAGE) technology produces large sets of interesting genes that are difficult to analyze directly. Bioinformatics tools are needed to interpret the functional information in these gene sets. We present an interactive web-based tool, called Gene Class, which allows functional annotation of SAG.. Read More»
- Genet. Mol. Res. 5(1):
SpotWhatR: a user-friendly microarray data analysis system
Authors: Tie Koide, Silvia M. Salem-Izacc, Suely L. Gomes and Ricardo Z.N. V�ªncio
SpotWhatR is a user-friendly microarray data analysis tool that runs under a widely and freely available R statistical language (http://www.r-project.org) for Windows and Linux operational systems. The aim of SpotWhatR is to help the researcher to analyze microarray data by providing basic tools for data visualization, normali.. Read More»
- Genet. Mol. Res. 5(1):
A fully resolved consensus between fully resolved phylogenetic trees
Authors: Jos�© Augusto Amgarten Quitzau and Jo�£o Meidanis
Nowadays, there are many phylogeny reconstruction methods, each with advantages and disadvantages. We explored the advantages of each method, putting together the common parts of trees constructed by several methods, by means of a consensus computation. A number of phylogenetic consensus methods are already known. Unfortunatel.. Read More»
- Genet. Mol. Res. 5(1):
Gene networks as a tool to understand transcriptional regulation
Authors: Diogo Fernando Veiga, F�¡bio Fernandes da Rocha Vicente and Gustavo Bastos
Gene regulatory networks, or simply gene networks (GNs), have shown to be a promising approach that the bioinformatics community has been developing for studying regulatory mechanisms in biological systems. GNs are built from the genome-wide high-throughput gene expression data that are often available from DNA microarray expe.. Read More»
- Genet. Mol. Res. 5(1):
An empirical examination of the standard errors of maximum likelihood phylogenetic parameters under the molecular clock via bootstrapping
Authors: Carlos G. Schrago
The molecular clock theory has greatly enlightened our understanding of macroevolutionary events. Maximum likelihood (ML) estimation of divergence times involves the adoption of fixed calibration points, and the confidence intervals associated with the estimates are generally very narrow. The credibility intervals are inferred.. Read More»
- Genet. Mol. Res. 5(1):