MIPSPlantsDB--plant database resource for integrative and comparative plant genome research

Abstract

Genome-oriented plant research delivers rapidly increasing amount of plant genome data. Comprehensive and structured information resources are required to structure and communicate genome and associated analytical data for model organisms as well as for crops. The increase in available plant genomic data enables powerful comparative analysis and integrative approaches. PlantsDB aims to provide data and information resources for individual plant species and in addition to build a platform for integrative and comparative plant genome research. PlantsDB is constituted from genome databases for Arabidopsis, Medicago, Lotus, rice, maize and tomato. Complementary data resources for cis elements, repetive elements and extensive cross-species comparisons are implemented. The PlantsDB portal can be reached at .

Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites

“…The alignment files were further used as input in the bioconductor package CAGEr version 1.2.9 for the following tasks: (1) to correct for G-addition when a mismatching G was encountered at the first position; (2) to estimate CAGE transcription start sites; (3) to cluster CAGE TSSs in nonoverlapping TSS clusters (Balwierz et al, 2009) and TCs in nonoverlapping regions; (4) to calculate expression values for dominant CTSSs (CTSS with the highest expression value in a given TC) and TCs in TPM after a power law-based normalization ; (5) to calculate the interquantile width, defined as the absolute distance in base pairs between positions of 10th and 90th percentile of the cumulative sum of CAGE tags for each TC; and (6) to determine differential usage of TSSs between tissues and between inbred lines (Haberle et al, 2014). To account for rRNA contamination, TC sequences were compared against the MIPS database (Mewes et al, 2002) of repetitive elements using BLAST (Spannagl et al, 2007;Camacho et al, 2009). Hits reaching the established threshold (E < 10 215 , 98% coverage and 98% similarity) were removed from further analyses.…”

Comprehensive Sequence Analysis of 24,783 Barley Full-Length cDNAs Derived from 12 Clone Libraries

“…The Morex BACs were downloaded using the keywords "Morex" and "BAC." After masking repeat sequences using RepeatMasker and the libraries of MIPS Repeat Element Database 4.3 (http://mips.helmholtz-muenchen.de/plant/genomes.jsp; Spannagl et al, 2007) and Triticeae Repeat Sequence Database release 10 (http://wheat.pw. usda.gov/ITMI/Repeats/), the FLcDNAs were mapped onto the BACs using the same method used for RAP annotation (Tanaka et al, 2008).…”

TriFLDB: A Database of Clustered Full-Length Coding Sequences from Triticeae with Applications to Comparative Grass Genomics

“…Thus, full-length cDNAs and their annotations provide an initial gateway to various omics data (Sakurai et al, 2005;Maeda et al, 2006). To respond to the increasing amount of plant genome data, user interfaces that provide a seamless integration of comparative functions will be required to perform knowledge mining not only within community databases for specified organisms, but also across datasets integrated with multiple plant species (Spannagl et al, 2007;Ware, 2007). Full-length cDNA resources and modeled proteomes should be integrated with various types of representative sequence resources not only in the same species, but also in related species, thereby making it possible to exchange genomic knowledge and gain insight from comparative genomics (Dong et al, 2005).…”