RESUMEN
Chromosome 2 of Plasmodium falciparum was sequenced; this sequence contains 947,103 base pairs and encodes 210 predicted genes. In comparison with the Saccharomyces cerevisiae genome, chromosome 2 has a lower gene density, introns are more frequent, and proteins are markedly enriched in nonglobular domains. A family of surface proteins, rifins, that may play a role in antigenic variation was identified. The complete sequencing of chromosome 2 has shown that sequencing of the A+T-rich P. falciparum genome is technically feasible.
Asunto(s)
Cromosomas/genética , Genes Protozoarios , Plasmodium falciparum/genética , Proteínas Protozoarias/genética , Análisis de Secuencia de ADN , Secuencia de Aminoácidos , Animales , Antígenos de Protozoos/química , Antígenos de Protozoos/genética , Composición de Base , Evolución Molecular , Genoma de Protozoos , Intrones , Proteínas de la Membrana/química , Proteínas de la Membrana/genética , Datos de Secuencia Molecular , Familia de Multigenes , Mapeo Físico de Cromosoma , Proteínas Protozoarias/química , ARN Protozoario/genética , ARN de Transferencia de Ácido Glutámico/genética , Secuencias Repetitivas de Ácidos Nucleicos , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Alineación de SecuenciaRESUMEN
GeneSplicer is a new, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been tested successfully using DNA from two reference organisms: the model plant Arabidopsis thaliana and human. It was compared to six programs representing the leading splice site detectors for each of these species: NetPlantGene, NetGene2, HSPL, NNSplice, GENIO and SpliceView. In each case GeneSplicer performed comparably to the best alternative, in terms of both accuracy and computational efficiency.
Asunto(s)
Algoritmos , Empalme Alternativo/genética , Biología Computacional/métodos , Arabidopsis/genética , ADN/genética , Bases de Datos Factuales , Genes/genética , Genoma Humano , Genoma de Planta , HumanosRESUMEN
MOTIVATION: The increased availability of genome sequences of closely related organisms has generated much interest in utilizing homology to improve the accuracy of gene prediction programs. Generalized pair hidden Markov models (GPHMMs) have been proposed as one means to address this need. However, all GPHMM implementations currently available are either closed-source or the details of their operation are not fully described in the literature, leaving a significant hurdle for others wishing to advance the state of the art in GPHMM design. RESULTS: We have developed an open-source GPHMM gene finder, TWAIN, which performs very well on two related Aspergillus species, A.fumigatus and A.nidulans, finding 89% of the exons and predicting 74% of the gene models exactly correctly in a test set of 147 conserved gene pairs. We describe the implementation of this GPHMM and we explicitly address the assumptions and limitations of the system. We suggest possible ways of relaxing those assumptions to improve the utility of the system without sacrificing efficiency beyond what is practical. AVAILABILITY: Available at http://www.tigr.org/software/pirate/twain/twain.html under the open-source Artistic License.
Asunto(s)
Algoritmos , Aspergillus/genética , Aspergillus/metabolismo , Mapeo Cromosómico/métodos , Perfilación de la Expresión Génica/métodos , Modelos Genéticos , Proteínas de Plantas/genética , Cadenas de Markov , Modelos Estadísticos , Programas InformáticosRESUMEN
Our aim was to find a formulation for pyramidon suppositories in which the physicochemical compatibility of the active substance with the excipient to be the highest. Fatty and hydrosoluble excipients were studied. Following up in time the quality of the obtained preparation, it was concluded that the fatty substances are preferable, the suppositories with glycero-gelatinous mass being more stable by an one hour freezing and two hours freeze drying.
Asunto(s)
Antipirina/química , Antipirina/administración & dosificación , Química Farmacéutica , Estabilidad de Medicamentos , Almacenaje de Medicamentos , Solubilidad , Supositorios , Factores de TiempoRESUMEN
UNLABELLED: We describe two new Generalized Hidden Markov Model implementations for ab initio eukaryotic gene prediction. The C/C++ source code for both is available as open source and is highly reusable due to their modular and extensible architectures. Unlike most of the currently available gene-finders, the programs are re-trainable by the end user. They are also re-configurable and include several types of probabilistic submodels which can be independently combined, such as Maximal Dependence Decomposition trees and interpolated Markov models. Both programs have been used at TIGR for the annotation of the Aspergillus fumigatus and Toxoplasma gondii genomes. AVAILABILITY: Source code and documentation are available under the open source Artistic License from http://www.tigr.org/software/pirate
Asunto(s)
Algoritmos , Perfilación de la Expresión Génica/métodos , Modelos Genéticos , Alineación de Secuencia/métodos , Análisis de Secuencia de ADN/métodos , Programas Informáticos , Animales , Aspergillus fumigatus/genética , Células Eucariotas , Cadenas de Markov , Modelos Estadísticos , Lenguajes de Programación , Toxoplasma/genéticaRESUMEN
Rice (Oryza sativa) is a model species for monocotyledonous plants, especially for members in the grass family. Several attributes such as small genome size, diploid nature, transformability, and establishment of genetic and molecular resources make it a tractable organism for plant biologists. With an estimated genome size of 430 Mb (Arumuganathan and Earle, 1991), it is feasible to obtain the complete genome sequence of rice using current technologies. An international effort has been established and is in the process of sequencing O. sativa spp. japonica var "Nipponbare" using a bacterial artificial chromosome/P1 artificial chromosome shotgun sequencing strategy. Annotation of the rice genome is performed using prediction-based and homology-based searches to identify genes. Annotation tools such as optimized gene prediction programs are being developed for rice to improve the quality of annotation. Resources are also being developed to leverage the rice genome sequence to partial genome projects such as expressed sequence tag projects, thereby maximizing the output from the rice genome project. To provide a low level of annotation for rice genomic sequences, we have aligned all rice bacterial artificial chromosome/P1 artificial chromosome sequences with The Institute of Genomic Research Gene Indices that are a set of nonredundant transcripts that are generated from nine public plant expressed sequence tag projects (rice, wheat, sorghum, maize, barley, Arabidopsis, tomato, potato, and barrel medic). In addition, we have used data from The Institute of Genomic Research Gene Indices and the Arabidopsis and Rice Genome Projects to identify putative orthologues and paralogues among these nine genomes.
Asunto(s)
Biología Computacional , Oryza/genética , Análisis de Secuencia de ADN , Secuencia de Bases , ADN de Plantas , Sistemas de Administración de Bases de Datos , Modelos Genéticos , Datos de Secuencia MolecularRESUMEN
Computational gene finding research has emphasized the development of gene finders for bacterial and human DNA. This has left genome projects for some small eukaryotes without a system that addresses their needs. This paper reports on a new system, GlimmerM, that was developed to find genes in the malaria parasite Plasmodium falciparum. Because the gene density in P. falciparum is relatively high, the system design was based on a successful bacterial gene finder, Glimmer. The system was augmented with specially trained modules to find splice sites and was trained on all available data from the P. falciparum genome. Although a precise evaluation of its accuracy is impossible at this time, laboratory tests (using RT-PCR) on a small selection of predicted genes confirmed all of those predictions. With the rapid progress in sequencing the genome of P. falciparum, the availability of this new gene finder will greatly facilitate the annotation process.