protein_evidence/
#all protein data were downloased from gramene.org

Arabidopsis_thaliana.TAIR10.27.pep.all.fa
wget ftp://ftp.gramene.org/pub/gramene/release46/data/fasta/arabidopsis_thaliana/pep/Arabidopsis_thaliana.TAIR10.27.pep.all.fa.gz

Brachypodium_distachyon.v1.0.27.pep.all.fa
wget ftp://ftp.gramene.org/pub/gramene/release46/data/fasta/brachypodium_distachyon/pep/Brachypodium_distachyon.v1.0.27.pep.all.fa.gz

Oryza_sativa.IRGSP-1.0.27.pep.all.fa
wget ftp://ftp.gramene.org/pub/gramene/release46/data/fasta/oryza_sativa/pep/Oryza_sativa.IRGSP-1.0.27.pep.all.fa.gz

Setaria_italica.JGIv2.0.27.pep.all.fa
wget ftp://ftp.gramene.org/pub/gramene/release46/data/fasta/setaria_italica/pep/Setaria_italica.JGIv2.0.27.pep.all.fa.gz

Sorghum_bicolor.Sorbi1.27.pep.all.fa
wget ftp://ftp.gramene.org/pub/gramene/release46/data/fasta/sorghum_bicolor/pep/Sorghum_bicolor.Sorbi1.27.pep.all.fa.gz

repeat_lib/
#This is the same repeat library used for the original maixe annotations with the helitrons removed.
#http://science.sciencemag.org/content/sci/326/5956/1112.full.pdf
Wessler-Bennetzen_2.fasta

transcript_evidence/
95_mRNA_seq_cdhit99.fa
#95 trinity-assembled publicly-available mRNA-seq data sets.
#Described here http://www.plantphysiol.org/content/167/1/25.long
#All of the assembled transcripts were combined and duplicates were filtered out using cdhit with a threshhold of 99%  

flcDNA_genbank.fa
#Full length cDNAs from genbank using this search parameter (FLI-CDNA[Keyword]) AND maize[Organism]

martin_seedling.fa
#Assembled transcripts from verry high coverage mRNA-sequencing of a maize seedling.
#Described here http://www.nature.com/articles/srep04519

wang_isoseq.fa
#IsoSeq transcripts generated from multiple tissues 
#Described here http://www.nature.com/articles/ncomms11708