03498nam a2200241 a 450000100080000000500110000800800410001910000170006024501230007726001800020030000190038050000200039952026990041965000110311865000110312965300300314065300090317065300150317965300160319465300130321065300090322370000240323215762462020-01-15       2009    bl uuuu     u00u1 u    #d1 aHERAI, R. H.  aA Web-based tool for identification and visualization of repetitive sequences within gene loci.h[electronic resource]  aIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCBc2009  aNão paginado.  aX-Meeting 2009.  aRecently the study of repetitive sequences in plant and animal genomes has gain momentum due many important biological mechanisms such as gene interference by RNAi and trans-splicing that seem to be mediated or influenced by the presence of repetitive sequences within the gene loci. Most part of repetitive sequences belong to intronic regions, and, usually, these studies have only mRNA sequences and they need the gene intron-exon structures, therefore it is necessary to map them back onto the studied organism reference genome in order to identify four matching pair types of repetitive sequences: direct repeat, inverted repeat, direct complementary repeat, and inverted complementary repeat. Although these steps are easily described, their computational implementation requires deep knowledge of the bioinformatics algorithms needed. In this work we present a WEB-based tool, called RepGraph, which integrates all the necessary steps to identify all matching pairs of repetitive sequences present in two gene loci, and graphically display their relationship in an intuitive graphical representation. Initially, the user must define two input mRNA sequences and associate them with one of the available organism genomes. Using Gmap, the mRNAs are mapped back onto genome in order to get their intron-exon structures, and their corresponding genomic sequence data. Finally, using NCBI-Bl2Seq, the repetitive sequences are identified and their relationship is analyzed by an ad hoc application module that generates a graphical visualization of the two input sequences, with colour coded intron-exon structures and their four matching pair types of repetitive sequences. RepGraph was usefully applied by Herai & Yamagishi (Brief. Bioinformatics, 2009) to confirm the presence of inverted complementary repeats within gene loci involved in inter-chromosomal trans-splicing. RepGraph is based on a free software methodology and it uses a 3-tier WEB software development model, in which the system architecture is split in three specific layers: user interface, business rules and persistence. The interaction between such layers follows a conceptual MVC model that is formed by a Controller component which coordinates the layers relationship. The system implementation was done with Java language v1.6, using the MVC Apache Struts framework. In despite of RepGraph be a WEB system, it was stored in a WEB Server with Tomcat v6.0 application server that treats user connections. External resources, like applications (GMap and NCBI-Bl2Seq) and genome databases, can be easily updated because they are defined in configuration files that are loaded and used by RepGraph to interact with user.  aGenome  aGenoma  aFerramenta baseada em web  aGmap  aModelo MVC  aNCBI-B12Seq  aRepGraph  aRNAi1 aYAMAGISHI, M. E. B.