laboratory of computational & structural biology

Our resources RSAT::Plants

blog: #!/perl/bioinfo

postal address
Laboratorio de Biología Computacional y Estructural, Estación Experimental Aula Dei-CSIC, Av. Montañana 1.005, 50059 Zaragoza (Spain)

phone (+34) 976716089

public transport logohow to get here
bicilogo rutas en bicicleta de Zaragoza al campus de Aula Dei
Research topics/objetivos del labo
Maximum-likelihood pan-genome phylogeny

Maximum-likelihood pan-genome phylogeny estimated with IQ-TREE from the consensus pan-genome clusters of Stenotrophomonas displayed in the Venn diagram

Vrs1 alleles

a) Alignment of Vrs1.b2, vrs1.a2, and Vrs1.b5 DNA partial sequences of exon 2. b) Multiple alignment of protein sequences of different alleles of the Vrs1 gene. c) Barley spikes from Spanish landraces SBCC039 (vrs1.a2) six-rowed (left) and SBCC155 (Vrs1.b5) two-rowed (right)

pangenome of Brachypodium distachyon

Gene-based pan-genome of Brachypodium distachyon. B,C) Core, softcore, shell, cloud genes. D) % coverage of 37,886 high-confidence pan-genes by short read data sets from 49 lines.

Nuclear and plastid filogenomic trees of <i>Brachypodium distachyon</i> ecotypes

Nuclear and plastid filogenomic trees of Brachypodium distachyon ecotypes.

pangenome Athaliana

Pan-genome of CDS annotated in 19 Arabidopsis thaliana ecotypes. A) Occupancy of CDS clusters. B) Pan-genome growth simulations. C) Mean expression of CDS in root, seedling and floral buds. D) dN/dS ratio of single-copy CDS clusters.

MEBS flowchart

Schematic representation of the 4 stages of the MEBS algorithm focusing on the Sulphur-cycle.

TF disordered residues vs tissues

Total disordered residues in transcription factors (PONDR VLS2b) vs number of tissues in several plant species.

barley drought experiment

Design of stress treatments and leaf water potential of barley SBCC073 (73) and Scarlett (SC) plants.

heterozygous mappings

Heterozygous mappings in barley occur when relevant loci are absent from the reference genome assembly.

nucleosome GFP

Model of nucleosome sandwich incorporating a single H2BGFP molecule (in red). The steric difficulty to accommodate the GFP tag increases if we consider that each nucleosome may contain up to two molecules of GFP.

interface annotation in footDB

Annotation of interface residues in footprintDB.

interfaces of R2R3 MYB TFs

(A) Sequence logos of the R2 and R3 recognition α-helices of Arabidopsis thaliana R2R3-MYB DBD subgroups (left) and of the bound cis-elements assayed on the Y1H experiments, classified into two groups (right).

BARLEYMAP pipeline

BARLEYMAP pipeline

plant disorder

Distribution of predicted disordered segments with length>30 in plants. Disorder in chloroplast (Cp), mitochondria (Mt) and nuclear (Nu) proteomes are shown.

footprint logo of restriction enzyme BamHI

footprint of dimeric complex 2bam_AB
(enzyme BamHI)

active transcriptional subnetworks in Escherichia coli

A few active transcriptional subnetworks in Escherichia coli (details here)

ML tree of plant-like FADS proteins

ML tree of plant-like FADS proteins (details here)

Multiple interface alignment of zinc fingers

Multiple interface alignment of zinc fingers (details here)

flowchart of DNAPROT footprint algorithm

DNAPROT algorithm (details here)

3D-fooprint of a comparative model of Escherichia coli FNR

structure-based position weight matrix for Escherichia coli FNR, modelled with TFmodeller
(read more here)

TFmodeller homology model of a protein-DNA complex

comparative model of a protein-DNA complex
(read more here)

evolutionary correlation between binding specificity and regulatory role in Bacteria

conceptual model of evolutionary role of binding specificity in bacterial regulatory networks
(read more here)

alpha parameter and codon usage table primers4clades benchmark

genomic benchmark of primers4clades
(read more here)

phylogenetic congruence heatmap

congruence of tree topologies derived from single and concatenated loci of Bradyrhizobium
(read more here)

flowchart of fragment-based homology modelling

benchmark of fragment-based comparative modelling approaches
(read more here)