RESUMO
The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank and sequence analysis tool BLAST. However, NCBI integrates many types of biomolecular data from variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries. Some tools though are resources specific and can be indirectly accessed from a particular database in the Entrez system. These include graphical viewers and comparative analysis tools such as TaxPlot, TaxMap and UniGene DDD (found via UniGene Homepage). Gene and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid and UniProt. There are many different ways of accessing genomic data at NCBI. Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources. This review article describes methods of accessing fungal genome data and provides examples that illustrate the use of analysis tools.
RESUMO
As more and more complete bacterial genome sequences become available, the genome annotation of previously sequenced genomes may become quickly outdated. This is primarily due to the discovery and functional characterization of new genes. We have reannotated the recently published genome of Shewanella oneidensis with the following results: 51 new genes have been identified, and functional annotation has been added to the 97 genes, including 15 new and 82 existing ones with previously unassigned function. The identification of new genes was achieved by predicting the protein coding regions using the HMM-based program GeneMark.hmm. Subsequent comparison of the predicted gene products to the non-redundant protein database using BLAST and the COG (Clusters of Orthologous Groups) database using COGNITOR provided for the functional annotation.
Assuntos
Proteínas de Bactérias/genética , Genoma Bacteriano , Shewanella/genética , Algoritmos , Proteínas de Bactérias/fisiologia , Biologia Computacional/métodos , Genes Bacterianos/genética , Genômica , Dados de Sequência Molecular , Fases de Leitura Aberta/genética , Alinhamento de Sequência/métodos , SoftwareRESUMO
In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI's Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, GeneMap'99, Human-Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP), SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheri-tance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih. gov.
Assuntos
Biotecnologia , Bases de Dados Factuais , Serviços de Informação , Animais , Perfilação da Expressão Gênica , Genoma , Genoma Humano , Humanos , Armazenamento e Recuperação da Informação , Internet , Biologia Molecular , National Institutes of Health (U.S.) , National Library of Medicine (U.S.) , Fenótipo , Alinhamento de Sequência , Estados UnidosRESUMO
The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http://www.ncbi.nlm.nih. gov/COG). In addition, a supplement to the COGs is available, in which proteins encoded in the genomes of two multicellular eukaryotes, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, and shared with bacteria and/or archaea were included. The new features added to the COG database include information pages with structural and functional details on each COG and literature references, improvements of the COGNITOR program that is used to fit new proteins into the COGs, and classification of genomes and COGs constructed by using principal component analysis.
Assuntos
Bases de Dados Factuais , Proteínas , Animais , Archaea/genética , Bactérias/genética , Caenorhabditis elegans/genética , Drosophila melanogaster/genética , Genoma , Armazenamento e Recuperação da Informação , Internet , Filogenia , Proteínas/classificação , Proteínas/genética , Saccharomyces cerevisiae/genética , Alinhamento de SequênciaRESUMO
We describe a genome annotation service provided by the Entrez browser, http://www.ncbi.nlm.nih.gov/entrez. All protein products identified in fully sequenced microbial genomes have been compared with proteins with known 3-D structure by use of the BLAST sequence comparison algorithm. For the approximately 20% of genome proteins in which unambiguous sequence similarity is detected, Entrez provides a link from the gene product to its predicted structure. The service uses the Cn3D molecular graphics viewer to present a 3-D view of the known structure, together with an alignment display mapping conserved residues from the genome protein onto the known structure. Using an example from Aeropyrum pernix, we illustrate how mapping to a 3-D structure can confirm predictions of biological function.
Assuntos
Bases de Dados Factuais , Genoma , Algoritmos , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/fisiologia , Gráficos por Computador , Coleta de Dados/instrumentação , Coleta de Dados/métodos , Bases de Dados Factuais/provisão & distribuição , Bases de Dados Factuais/tendências , Genoma Bacteriano , Modelos Moleculares , Dados de Sequência Molecular , Estrutura Quaternária de ProteínaRESUMO
In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval and resources that operate on the data in GenBank and a variety of other biological data made available through NCBI's Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing pages, GeneMap'99, Davis Human-Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP) pages, Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP) pages, SAGEmap, Online Mendelian Inheritance in Man (OMIM) and the Molecular Modeling Database (MMDB). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih. gov
Assuntos
Biologia , Bases de Dados Factuais , Animais , Expressão Gênica , Genoma Humano , Humanos , Armazenamento e Recuperação da Informação , Camundongos , Modelos Moleculares , National Library of Medicine (U.S.) , Neoplasias/genética , Fenótipo , Estados UnidosRESUMO
MOTIVATION: The large amount of genome sequence data now publicly available can be accessed through the National Center for Biotechnology Information (NCBI) Entrez search and retrieval system, making it possible to explore data of a breadth and scope exceeding traditional flatfile views. RESULTS: Here we report recent improvements for completely sequenced genomes from viruses, bacteria, and yeast. Flexible web based views, precomputed relationships, and immediate access to analytical tools provide scientists with a portal into the new insights to be gained from completed genome sequences. AVAILABILITY: Entrez Genomes can be accessed on the World Wide Web at http://www.ncbi.nlm.nih.gov/Entrez/Genome/ org.html.
Assuntos
Bases de Dados Factuais , Genoma , Internet , Sequência de Aminoácidos , Cromossomos/genética , Genoma Arqueal , Genoma Bacteriano , Genoma Fúngico , Genoma Viral , Dados de Sequência Molecular , National Library of Medicine (U.S.) , Fases de Leitura Aberta , Proteínas/classificação , Proteínas/genética , Alinhamento de Sequência , Estados UnidosRESUMO
'BLAST 2 Sequences', a new BLAST-based tool for aligning two protein or nucleotide sequences, is described. While the standard BLAST program is widely used to search for homologous sequences in nucleotide and protein databases, one often needs to compare only two sequences that are already known to be homologous, coming from related species or, e.g. different isolates of the same virus. In such cases searching the entire database would be unnecessarily time-consuming. 'BLAST 2 Sequences' utilizes the BLAST algorithm for pairwise DNA-DNA or protein-protein sequence comparison. A World Wide Web version of the program can be used interactively at the NCBI WWW site (http://www.ncbi.nlm.nih.gov/gorf/bl2.++ +html). The resulting alignments are presented in both graphical and text form. The variants of the program for PC (Windows), Mac and several UNIX-based platforms can be downloaded from the NCBI FTP site (ftp://ncbi.nlm.nih.gov).
