This reports the protocol used to align the Maize_Seq_Panzea features to tigrv4-genome. Fri Apr 14 11:46:02 2006 Source of Maize_Seq_Panzea : Obtained from panzea project Alignment procedure details --------------------------- 3092 Maize_Seq_Panzea are aligned to tigrv4-genome using blat with blat parameters -minIdentity=50 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'CrossSpecies-Coding' data sets. Initial summary # alignments : 2488 # unique Features these alignments represent: 2432 % of total features these alignments represent : 78.65 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 139 150 192 200 235 250 219 300 194 350 223 400 216 450 148 500 123 550 113 600 78 650 72 700 65 750 66 800 63 10000 342 Alignments with matches less than 150 bp are deleted # remaining Alignments : 2159 # unique Features these remaining alignments represent: 2121 % of total features these alignments represent : 68.60 % Frequency distribution of the remaining features # hits # features -------- -------- 1 2096 2 21 3 2 4 1 5 0 6 0 8 0 9 0 10 0 20 1 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 2144 # unique Features these remaining alignments represent: 2119 % of total features these alignments represent : 68.53 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 0 40 0 50 0 60 2 70 8 80 201 90 1666 95 263 100 4 Following is the distribution of gaps Gaps # features -------- -------- 1000 1373 2000 394 3000 190 4000 88 5000 36 6000 16 7000 9 8000 8 9000 3 10000 1 Following is the final summary # alignments : 2144 # unique Features these alignments represent: 2119 % of total features these alignments represent : 68.53 %