Computational & structural biology software
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Web resources
- RSAT::Plants: A plant-dedicated server for the analysis of regulatory sequences
- BARLEYMAP: a tool to search the position of barley genetic markers on the Barley Physical Map and the POPSEQ map
- footprintDB: a database of transcription factors with annotated cis elements and binding interfaces
- 3D-footprint: a database for the structural analysis of protein-DNA complexes
- barley_pangenes: clusters of gene models/alleles in a similar genomic location
Source code, binaries and Docker containers
- plant-scripts: code examples for interrogating Ensembl Plants from your own scripts, masking & annotating repeats and calling pangenes in plant genomes (GitHub downloads).
- GET_HOMOLOGUES: a versatile software package for pan-genome analysis (Linux/MacOSX Perl, R scripts, binaries, bioconda, Docker image, manual, microbia, plants, GitHub downloads)
- GET_PHYLOMARKERS: software package designed to identify optimal genomic markers for phylogenomics, population genetics and genomic taxonomy.
- coexpression_motif_discovery: recipes to discover cis-regulatory motifs within proximal promoters of plants in RSAT::Plants.
- Multigenomic Entropy-Based Score (MEBS): protocol for finding informative protein families and then using them to score metagenomic sets (PDF)
- Chloroplast assembly protocol: set of scripts for the assembly of chloroplast genomes out of whole-genome sequencing reads
- DNAPROT: takes protein-DNA complex in PDB format and calculates structure-based position weight matrices (manual), [Docker]
- primers4clades: PCR primers for cross-species amplification of sequences from metagenomic DNA or selected lineages [legacy Docker]
- TFcompare: a tool for structural alignment of DNA motifs and protein domains from DNA-binding protein complexes [legacy Docker]
- TFmodeller: comparative modelling of protein-DNA complexes [legacy Docker]
Assorted utilities
- split_pairs: efficient kseq-based program to sort and find paired reads within FASTQ/FASTA files, with the ability to edit headers with the power of Perl-style regular expressions
- split_blast: Perl script to take advantage of multi-core CPUs for doing BLAST searches that fit in RAM (also part of GET_HOMOLOGUES)
- addCDD2genbank.pl: adds domain annotations from CDD to protein sequences contained in CDS features within input GenBank file
- xmfa2fasta.pl: reads in XMFA file produced by progressive MAUVE and produces a multi-FASTA file containing a multiple sequence alignment
- see all scripts
Data files
Available here
GitHub repositories
Main: https://github.com/eead-csic-compbio
Other repos with code contributed by members of the lab: