Um conjunto de ferramentas para a compara??o de genomas completos de bact?rias baseada em genes.

Most of the computational biology analysis is made comparing genomic features. The nucleotide and amino acid sequence alignments are frequently used in gene function identification and genome comparison. Despite its widespread use, there are limitations in their analysis capabilities that need to be considered but are often overlooked or unknown by many researchers. This paper presents a gene based whole genome comparison toolkit which can be used not only as an alternative and more robust way to compare a set of whole genomes, but, also, to understand the tradeoff of the use of sequence local alignment in this kind of comparison. A study case was performed considering fifteen whole genomes of the Xanthomonas genus. The results were compared with the 16S rRNA-processing protein RimM phylogeny and some thresholds for the use of sequence alignments in this kind of analysis were discussed.Grande parte das analises realizadas na biologia computacional ? feita comparando caracter?sticas gen?micas. Os alinhamentos de nucleot?deos e de amino?cidos s?o frequentemente usados na identifica??o de fun??es g?nicas e na compara??o de genomas. Apesar de seu uso generalizado, h? limita??es em suas capacidades de analise que precisam ser consideradas, mas s?o frequentemente negligenciadas ou desconhecidas por muitos pesquisadores. Este artigo apresenta um conjunto de ferramentas de compara??o de genomas completos baseado em genes que pode ser usado n?o somente como uma maneira alternativa e mais robusta de comparar um conjunto de genomas completos, mas tamb?m para entender as vantagens e desvantagens do uso do alinhamento local de sequencias neste tipo de compara??o. Um estudo de caso foi realizado considerando quinze genomas completos do g?nero Xanthomonas. Os resultados foram comparados com a filogenia produzida utilizando a prote?na 16S rRNA-processing protein RimM e alguns limiares para o uso de alinhamentos de sequencias neste tipo de analise foram discutidos

Genetic evaluation for egg mass in partial periods and complete period in meat quails

The objective of this study was to obtain estimates of genetic and phenotypic parameters for egg mass of meat quails and also to propose an optimal age for selection of birds through the egg mass. The data used in this study came from 3,503 female meat quails (UFV1: 1.811 quails; UFV2: 1.692 quails) of the Poultry Breeding Program from Universidade Federal de Viçosa. The traits examined were egg mass in partial periods until 77, 112, 147 and 182 days, and egg mass in the total period of 407 days by the use of single and bi-trait animal models. For the genetic group UFV1, the heritability values for the periods were high: 0.58, 0.59, 0.57, 0.59 and 0.24 (until 77, 112, 147,182 and 407 days, respectively). The values of genetic correlations were medium, ranging from 0.51 (77 and 407 days) to 0.61 (112 and 407, 147 and 407 days). For the genetic group UFV2, the estimates of heritability were of low magnitude: 0.05, 0.03, 0.04, 0.05, and 0.11 (until 77, 112, 147, 182, and 407 days, respectively). The values for genetic correlation ranged from 0.61 (112 and 407 days) to 0.93 (77 and 407 days). For the genetic group UFV1, the second partial period (112 days) for selection of meat quails using the egg mass trait is recommended, due to a higher value of heritability and a higher value of genetic correlation with the total and relative efficiency close to the unity in this period. In the genetic group UFV2, the first partial period (77 days) is indicated, since it had a higher estimation of genetic correlation and a higher relative efficiency. The choice of these partial periods reduces the generation interval, increasing the intensity of selection and an increase in genetic gain per unit of time

Heterogeneidade de variância residual em modelos de regressão aleatória na descrição do crescimento de codornas de corte

Para comparar a influência da heterogeneidade da variância residual nos parâmetros genéticos estimados para a curva de crescimento de codornas de corte, foram utilizados dados provenientes de 26.835 e 27.447 observações, de 3.909 e 4.040 codornas de corte das linhagens UFV-1 e UFV-2, respectivamente. Foi avaliado o peso corporal nas duas linhagens, aos 1, 7, 14, 21, 28, 35 e 42 dias de idade, por meio de modelo animal em regressão aleatória, considerando na modelagem as variâncias residuais em classes de idades. Observou-se aumento no Log e L, significativo pelo teste da razão de verossimilhança (LRT), com o aumento do número de classes heterogêneas. Na modelagem da variância residual, foram consideradas classes de idade: homogênea: CL1 (uma classe): 1-42 dias; e as heterogêneas: CL2 (duas classes): 1 e 7-42 dias; CL3 (três classes): 1, 7 e 14-42 dias; CL4 (quatro classes): 1, 7, 14 e 21-42 dias; CL5 (cinco classes): 1, 7, 14 e 21 e 28-42 dias; CL6 (seis classes): 1, 7, 14, 21, 28 e 35-42 dias; CL7 (sete classes): 1, 7, 14, 21, 28, 35 e 42 dias de idade. O modelo que considerou homogeneidade de variância residual mostrou-se inadequado. As estimativas de variâncias, herdabilidades e correlações foram influenciadas pela modelagem da variância residual. A utilização de heterogeneidade de variância residual (CL7) para modelar as variâncias associadas à curva de crescimento das codornas de corte é necessária

Genetic parameters for egg production in meat quails through partial periods

ABSTRACT: We estimated genetic and phenotypic parameters for egg production in meat-type quails aiming to propose an optimal age for selection through partial record egg production. Data of 3,503 female quails from two strains (namely, UFV1, with 1,811 and UFV2 with 1,692 females) were used. Egg production was assessed by the number of eggs recorded after 42 days of age and each partial period consisted on 35 days of egg production forward. Covariance components were estimated by using single and bivariate animal model, comprising each partial period of egg production and full egg production period (one year of egg laying). Regarding strain UFV1, heritability estimates ranges from 0.03 to 0.16, and for strain UFV2 0.20 to 0.25. The highest genetic correlation with full egg production was with second period (0.64) for strain UFV1 and with third period (0.47) for UFV2. Therefore, animal selection based on egg production until 112 days for the strain UFV1 and 147 days for the strain UFV2 provided increased genetic gain by reducing generation interval