• TRANSFAC

  • Referenced in 73 articles [sw17201]
  • database on transcription factors, their genomic binding sites and DNA-binding profiles (http://transfac.gbf.de/TRANSFAC/ ... matrices as well as by data on plant sites and factors. Moreover, TRANSFAC has been...
  • PlantTFDB

  • Referenced in 4 articles [sw17023]
  • covers the main lineages of green plants, providing genomic TF repertoires across green plants...
  • MAKER-P

  • Referenced in 1 article [sw17330]
  • creation, management, and quality control of plant genome annotations. We have optimized and extended ... MAKER in order to better support plant genome annotation efforts. New features include better parallelization ... large repeat-rich plant genomes, noncoding RNA annotation capabilities, and support for pseudogene identification ... even Arabidopsis, perhaps the best-annotated plant genome. We have also installed and benchmarked MAKER...
  • RepeatExplorer

  • Referenced in 1 article [sw23829]
  • RepeatExplorer: a galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from ... makes up large portions of plant and animal nuclear genomes, yet it remains the least ... uses short sequences randomly sampled from the genome as input, it is ideal for analyzing ... medium copy repeats in higher plant genomes...
  • MCScanX

  • Referenced in 1 article [sw29671]
  • algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal ... Applications of MCScanX to several sequenced plant genomes and gene families are shown as examples...
  • Signal-3L

  • Referenced in 16 articles [sw26857]
  • protein sequences generated in the post-genomic era, the challenge has become even more urgent ... sequences and their cleavage sites in human, plant, animal, eukaryotic, Gram-positive, and Gram-negative...
  • Diurnal

  • Referenced in 5 articles [sw29307]
  • genome-wide expression results of genes from several array experiments conducted on common model plants...
  • GeneSplicer

  • Referenced in 5 articles [sw17323]
  • system for detecting splice sites in the genomic DNA of various eukaryotes. The system ... from two reference organisms: the model plant Arabidopsis thaliana and human. It was compared...
  • VirtualLeaf

  • Referenced in 3 articles [sw28766]
  • Modeling of Plant Tissue Growth and Development. Plant organs, including leaves and roots, develop ... mechanisms complicate classic molecular genetics or functional genomics approaches to biological development, because these methodologies ... traits at the level of the whole plant or organ. Instead, understanding gene function requires...
  • GWAPP

  • Referenced in 1 article [sw29292]
  • GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis. Arabidopsis thaliana ... plants. Its highly selfing nature, small size, short generation time, small genome size, and wide...
  • GATB

  • Referenced in 2 articles [sw33135]
  • Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly efficient algorithms ... kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes...
  • SSRscanner

  • Referenced in 1 article [sw14825]
  • genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range ... distributed almost at random throughout the genome, ranging from mononucleotide to trinucleotide repeats. They...
  • synbreed

  • Referenced in 0 articles [sw17098]
  • genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding...
  • AceView

  • Referenced in 3 articles [sw23000]
  • sequences are first co-aligned on the genome then clustered into a minimal number ... relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred...
  • BaCelLo

  • Referenced in 6 articles [sw17174]
  • subcellular location of proteins in large scale genomic projects. Results. BaCelLo is a predictor ... kingdom-specific predictors are implemented: for animals, plants and fungi, respectively. When distributing the proteins...
  • EdiPy

  • Referenced in 1 article [sw01955]
  • appropriately designed to simulate the evolution of plant mitochondrial genes in a biologically realistic fashion ... provides multiple artificial alignments corresponding to both genomic and cDNA sequences. Each artificial data...
  • MetNet

  • Referenced in 2 articles [sw25662]
  • available software in development for analysis of genome-wide RNA, protein and metabolite profiling data ... metabolic and regulatory networks that control plant composition and development...
  • Maple

  • Referenced in 4919 articles [sw00545]
  • The result of over 30 years of cutting...
  • Mathematica

  • Referenced in 5703 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 11496 articles [sw00558]
  • MATLAB® is a high-level language and interactive...