RESUMO
Splicing is one of the major contributors to observed spatiotemporal diversification of transcripts and proteins in metazoans. There are numerous factors that affect the process, but splice sites themselves along with the adjacent splicing signals are critical here. Unfortunately, there is still little known about splicing in plants and, consequently, further research in some fields of plant molecular biology will encounter difficulties. Keeping this in mind, we performed a large-scale analysis of splice sites in eight plant species, using novel algorithms and tools developed by us. The analyses included identification of orthologous splice sites, polypyrimidine tracts and branch sites. Additionally we identified putative intronic and exonic cis-regulatory motifs, U12 introns as well as splice sites in 45 microRNA genes in five plant species. We also provide experimental evidence for plant splice sites in the form of expressed sequence tag and RNA-Seq data. All the data are stored in a novel database called ERISdb and are freely available at http://lemur.amu.edu.pl/share/ERISdb/.
Assuntos
Bases de Dados Genéticas , Genes de Plantas , Sítios de Splice de RNA , RNA de Plantas/genética , Software , Algoritmos , Etiquetas de Sequências Expressas , Internet , Íntrons , MicroRNAs/genética , Plantas/genética , Splicing de RNA , Sequências Reguladoras de Ácido Ribonucleico , Ferramenta de Busca , Análise de Sequência de RNA , Transdução de SinaisRESUMO
Genomes of organisms contain a variety of repeated structures of various length and type, interspersed or tandem. Tandem repeats play important role in molecular biology as they are related to genetic backgrounds of inherited diseases, and also they can serve as markers for DNA mapping and DNA fingerprinting. Improving the efficiency of algorithms for searching for tandem repeats in DNA sequences can lead to many useful applications in the area of genomics. We introduce a very efficient, web-based tool for large scale searching for exact tandem repeats in genomes, based on the use of the Burrows-Wheeler Transform. The service is a remarkably efficient and powerful application that allows analyzing complete genomes without any restrictions. The Burrows-Wheeler Tandem Repeat Searcher (BWtrs) is an on-line application that searches for the exact occurrences of tandem repetitions in DNA sequences. The BWtrs service is freely available at: http://bioinfo.polsl.pl/BWtrs. We present examples of the use of our web application and we compare results of our computations with the results obtained by using other existing tools for searches for exact tandem repeats.
Assuntos
Galinhas/genética , Biologia Computacional/métodos , Genoma Humano/genética , Sequências de Repetição em Tandem , Algoritmos , Animais , Sequência de Bases , Humanos , Internet , SoftwareRESUMO
The explosive growth in biological data in recent years has led to the development of new methods to identify DNA sequences. Many algorithms have recently been developed that search DNA sequences looking for unique DNA sequences. This paper considers the application of the Burrows-Wheeler transform (BWT) to the problem of unique DNA sequence identification. The BWT transforms a block of data into a format that is extremely well suited for compression. This paper presents a time-efficient algorithm to search for unique DNA sequences in a set of genes. This algorithm is applicable to the identification of yeast species and other DNA sequence sets.
Assuntos
Algoritmos , Biologia Computacional/métodos , DNA/química , DNA/classificação , Compressão de Dados/métodos , Reconhecimento Automatizado de Padrão/métodos , Análise de Sequência de DNA/métodos , Leveduras/isolamento & purificação , Sequência de Bases , DNA/análise , Sistemas de Gerenciamento de Base de Dados , Bases de Dados Genéticas , Dados de Sequência Molecular , Sequências Repetitivas de Ácido NucleicoRESUMO
Genomic sequences contain a variety of repeated structures of various lengths and types, interspersed or in tandem. Repetitive structures play an important role in molecular biology; they are related to the genetic backgrounds of inherited diseases, and they can also serve as markers for DNA mapping and DNA fingerprinting. Since biological databases keep growing in size and number there is a need for creating new tools for finding repeats in genomic sequences. This paper presents a new method for searching for tandem repeats in DNA sequences. It is based on the Burrows-Wheeler Transform (BWT), a very fast and effective data compression algorithm.