6 Result(s)
within
Protocol
Bruno Contreras-Moreira
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Protocol
Pangenome Analysis of Plant Transcripts and Coding Sequences
The pangenome of a species is the sum of the genomes of its individuals. As coding sequences often represent only a small fraction of each genome, analyzing the pangene set can be a cost-effective strategy for...
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Protocol
Scripting Analyses of Genomes in Ensembl Plants
Ensembl Plants (http://plants.ensembl.org) offers genome-scale information for plants, with four releases per year. As of release 47 (April 2020) it features 79 species ...
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Protocol
FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces
FootprintDB is a database and search engine that compiles regulatory sequences from open access libraries of curated DNA cis-elements and motifs, and their associated transcription factors (TFs). It systematic...
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Protocol
RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes
In this protocol, we explain how to run ab initio motif discovery in order to gather putative transcription factor binding motifs (TFBMs) from sets of genomic regions returned by ChIP-seq experiments. The protoco...
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Protocol
RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes
The plant-dedicated mirror of the Regulatory Sequence Analysis Tools (RSAT, http://plants.rsat.eu) offers specialized options for researchers dealing with plant tr...
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Protocol
Robust Identification of Orthologues and Paralogues for Microbial Pan-Genomics Using GET_HOMOLOGUES: A Case Study of pIncA/C Plasmids
GET_HOMOLOGUES is an open-source software package written in Perl and R to define robust core- and pan-genomes by computing consensus clusters of orthologous gene families from whole-genome sequences using the...
