MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in MetazoaReport as inadecuate




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BMC Bioinformatics

, 7:36

First Online: 24 January 2006Received: 03 May 2005Accepted: 24 January 2006

Abstract

BackgroundMitochondria are sub-cellular organelles that have a central role in energy production and in other metabolic pathways of all eukaryotic respiring cells. In the last few years, with more and more genomes being sequenced, a huge amount of data has been generated providing an unprecedented opportunity to use the comparative analysis approach in studies of evolution and functional genomics with the aim of shedding light on molecular mechanisms regulating mitochondrial biogenesis and metabolism.

In this context, the problem of the optimal extraction of representative datasets of genomic and proteomic data assumes a crucial importance. Specialised resources for nuclear-encoded mitochondria-related proteins already exist; however, no mitochondrial database is currently available with the same features of MitoRes, which is an update of the MitoNuc database extensively modified in its structure, data sources and graphical interface. It contains data on nuclear-encoded mitochondria-related products for any metazoan species for which this type of data is available and also provides comprehensive sequence datasets gene, transcript and protein as well as useful tools for their extraction and export.

DescriptionMitoRes http:-www2.ba.itb.cnr.it-MitoRes- consolidates information from publicly external sources and automatically annotates them into a relational database. Additionally, it also clusters proteins on the basis of their sequence similarity and interconnects them with genomic data. The search engine and sequence management tools allow the query-retrieval of the database content and the extraction and export of sequences gene, transcript, protein and related sub-sequences intron, exon, UTR, CDS, signal peptide and gene flanking regions ready to be used for in silico analysis.

ConclusionThe tool we describe here has been developed to support lab scientists and bioinformaticians alike in the characterization of molecular features and evolution of mitochondrial targeting sequences. The way it provides for the retrieval and extraction of sequences allows the user to overcome the obstacles encountered in the integrative use of different bioinformatic resources and the completeness of the sequence collection allows intra- and interspecies comparison at different biological levels gene, transcript and protein.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-7-36 contains supplementary material, which is available to authorized users.

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Author: Domenico Catalano - Flavio Licciulli - Antonio Turi - Giorgio Grillo - Cecilia Saccone - Domenica D-Elia

Source: https://link.springer.com/



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