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      Analysis of the Macaca mulatta transcriptome and the sequence divergence between Macaca and human

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          Abstract

          Putative Macaca mulata orthologs for over 6,000 human genes have been sequenced from eleven tissues and three species of macaque. Macaque inter- and intraspecific nucleotide diversity is also reported.

          Abstract

          We report the initial sequencing and comparative analysis of the Macaca mulatta transcriptome. Cloned sequences from 11 tissues, nine animals, and three species ( M. mulatta, M. fascicularis, and M. nemestrina) were sampled, resulting in the generation of 48,642 sequence reads. These data represent an initial sampling of the putative rhesus orthologs for 6,216 human genes. Mean nucleotide diversity within M. mulatta and sequence divergence among M. fascicularis, M. nemestrina, and M. mulatta are also reported.

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          Gene Ontology: tool for the unification of biology

          Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)
          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.

            Geo M Pertea, Xiaoqiu Huang, Feng Liang … (2003)
            TGICL is a pipeline for analysis of large Expressed Sequence Tags (EST) and mRNA databases in which the sequences are first clustered based on pairwise sequence similarity, and then assembled by individual clusters (optionally with quality values) to produce longer, more complete consensus sequences. The system can run on multi-CPU architectures including SMP and PVM.
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              Database resources of the National Center for Biotechnology.

              D Wheeler (2003)
              In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). 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.
              Article 0 comments Cited 305 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central (London )
                ISSN (Print): 1465-6906
                ISSN (Electronic): 1465-6914
                Publication date (Print): 2005
                Publication date (Electronic): 30 June 2005
                Volume: 6
                Issue: 7
                Page: R60
                Affiliations
                [1 ]Illumigen Biosciences Inc., Suite 450, 2203 Airport Way South, Seattle, WA 98134, USA
                [2 ]Department of Microbiology, University of Washington, Seattle, WA 98195-8070, USA
                [3 ]Washington National Primate Research Center, University of Washington, Seattle, WA 98195-8070, USA
                Article
                Publisher ID: gb-2005-6-7-r60
                DOI: 10.1186/gb-2005-6-7-r60
                PMC ID: 1175991
                PubMed ID: 15998449
                SO-VID: 07078008-dc29-4ea8-a58f-2737b9590416
                Copyright © Copyright © 2005 Magness et al.; licensee BioMed Central Ltd.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 18 January 2005
                Date revision received : 4 April 2005
                Date accepted : 23 May 2005
                Categories
                Subject: Method

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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