Pan-gene analysis
=================

Files:
  MaizeGDB_B73_pangene_2020_11.tsv.gz   - pan-genes across all B73 assembly versions
                                          Updated 07/01/21: includes DAGchainer analysis
  MaizeGDB_maize_pangene_2020_08.tsv.gz - pan-genes across all genome assemblies 
                                          hosted at MaizeGDB

Format:
  One pan-gene per line.

  Column 1:      A random identifier for the pan-gene.
  Columns 2-end: Gene model members of the pan-gene. Note that some pan-genes have
                 multiple gene models from the same assembly.

  See the file MaizeGDB_maize_pangene.xref for the cross reference between genome
  assembly names and gene model prefixes. 

Methods:
Gene model CDS transcripts for each genome were pairwise aligned to all other 
genomes using:
   blastn -perc_identity 95 -evalue 1e-10 -outfmt "6 std qlen slen qcovs". 

Syntenic orthologs of pairwise alignment outputs were found using DagChainer 
with parameters -D 1000000 -g 40000 -A 4.

All DagChainer pairwise syntenic ortholog outputs were then concatenated and 
run through the program MCL with the parameters -I 2.0 -te 20 --abc -o