
protein->mRNA->genome tests:
    *MRnaProt.map - map of mRNA to associated protein
    *Prot.fa  - protein sequence
    *MRna.fa  - mRNA sequence
    *MRna.psl - mRNA alignment to genome
    *ProtMRna.blast - blast alignment of protein to mRNA (plus some other hits)


  - alignments of protein to mrna were done with:
    formatdb -i kgMRna.fa -p F
    blastall -S 2 -p tblastn -d kgMRna.fa -i kgProt.fa -o kgProtMRna.blast

  - test PSLs are generated from tblastn output in this directory when
    test is run to allow for changes in blastToPsl

  - test sets:
    - kg*: input: basic set of mRNAs and proteins
    - gapBoth*: both query and target have a gap between two blocks

mRNA->mRNA->DNA mapping test:
  pos strand:
    BC032429, AY211386, AK000004, BX647829, AX810690 -> NM_033086  -> genome
  neg strand:
    AB000114, BC046356 -> NM_005014 -> genome

  refSeqGen.psl - refseq to genome alignments
  mrnaRefSeq.psl - rna to refseq alignments, created with
        blat -noHead rs.fa gb.fa mrnaRefSeq.psl

  mrnaRefSeqX.psl - rrna to refseq translated alignments, created with
        blat -noHead -q=rnax -t=dnax rs.fa gb.fa mrnaRefSeqX.psl

retro/parent alignment with -simplifyMappingIds
  parent.psl, retro.psl from hg18
