2005/08/03 - JK notes on setting alignment parameters

assembly   srcDb    cdnaType  orgCat  minId  minCover  localNBest  minQSize  minNonRep  polyASizes  polyTSizes
finished   refseq   mrna      native  0.96   0.25      0.001       20        16         yes         no
finished   refseq   mrna      xeno    0.35   0.25      0.010       20        40         yes         no
finished   genbank  mrna      native  0.96   0.25      0.005       20        16         yes         no
finished   genbank  mrna      xeno    0.35   0.25      0.010       20        40         yes         no
finished   genbank  est       native  0.96   0.25      0.005       20        16         yes         yes
finished   genbank  est       xeno    0.10   0.10      0.010       20        40         yes         yes

assembly   srcDb    cdnaType  orgCat  minId  minCover  localNBest  minQSize  minNonRep  polyASizes  polyTSizes
wellOrder  refseq   mrna      native  0.95   0.15      0.001       20        same       same        same
wellOrder  refseq   mrna      xeno    0.35   0.15      0.010       20                               
wellOrder  genbank  mrna      native  0.95   0.15      0.005       20                               
wellOrder  genbank  mrna      xeno    0.35   0.15      0.010       20                               
wellOrder  genbank  est       native  0.95   0.15      0.005       20                               
wellOrder  genbank  est       xeno    0.35   0.10      0.010       20                               

assembly   srcDb    cdnaType  orgCat  minId  minAliSz  localNBest  minQSize  minNonRep  polyASizes  polyTSizes
lowCover   refseq   mrna      native  0.94   80        same        same      same       same        same
lowCover   refseq   mrna      xeno    0.33   80                                                     
lowCover   genbank  mrna      native  0.94   80                                                     
lowCover   genbank  mrna      xeno    0.33   80                                                     
lowCover   genbank  est       native  0.94   50                                                     
lowCover   genbank  est       xeno    0.33   50                                                     


Previous special cases

refseq.mrna.xeno for panTro1, rheMac1:
    -minCover=0.15 -minId=0.94 -localNearBest=0.001
    plus there are hacks for panTro1 to treat human mRNAs
    as the only xeno category and use native blat parameters.

refseq.mrna.xeno for canFam1, canFam2, dasNov1, dp2, dp3, droAna1, droAna2,
                     droGri1, droMoj1, droMoj2, droSim1, droYak1, echTel1,
                     loxAfr1, oryCun1
    -minId=0.75 -minCover=0.15 -localNearBest=0.005

refseq.mrna.xeno for ci1, ci2, strPur1
    -minId=0.15 -minCover=0.25 -localNearBest=0.005

ones with xeno ests:
     hg16,hg17, mm5, mm6, rn3, panTro1
