Computational & structural biology software
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Web resources
- RSAT::Plants: server for the analysis of regulatory sequences in plant genomes (available also as Docker container).
- BARLEYMAP: a tool to search the position of genetic markers on barley genomic, physical and POPSEQ maps.
- barley_pangenes: clusters of gene models/alleles in a similar genomic location, linked from BARLEYMAP.
- PRUNUSMAP: a tool to search the position of genetic markers and protein on annotated Prunus genomes.
- footprintDB: a
database of transcription factors with annotated cis elements and
binding interfaces. Includes our own databases
- 3D-footprint, which runs structural analysis of protein-DNA complexes from the Protein Data Bank.
- EEADannot, with manually curated DNA motifs and cis regulatory sites, mostly from plants.
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 gene-based pangenome analysis of microbes and plants (Linux/MacOSX Perl, R scripts, binaries, bioconda, [Docker], manuals and tutorials, GitHub downloads).
GET_PHYLOMARKERS: software package designed to identify optimal genomic markers for phylogenomics, population genetics and genomic taxonomy.
[RSAT Docker]: ready-to-use, requires downloading/installing genomes (see docs and protocol for coexpression motif discovery in plants).
Multigenomic Entropy-Based Score (MEBS): protocol for finding informative protein families and then using them to score metagenomic sets.
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), [legacy 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: