This reports the protocol used to align the Maize_ESTcluster_MMPconsensus features to tigrv4-genome. Fri Apr 14 11:49:21 2006 Source of Maize_ESTcluster_MMPconsensus : MaizeDB Unigenes, these are obtained from Mary Polacco ??? Alignment procedure details --------------------------- 10678 Maize_ESTcluster_MMPconsensus 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 : 8286 # unique Features these alignments represent: 8111 % of total features these alignments represent : 75.96 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 630 150 744 200 871 250 841 300 752 350 693 400 620 450 487 500 409 550 308 600 243 650 233 700 194 750 196 800 142 10000 923 Alignments with matches less than 150 bp are deleted # remaining Alignments : 6934 # unique Features these remaining alignments represent: 6805 % of total features these alignments represent : 63.73 % Frequency distribution of the remaining features # hits # features -------- -------- 1 6701 2 95 3 4 4 2 5 0 6 2 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 : 6903 # unique Features these remaining alignments represent: 6800 % of total features these alignments represent : 63.68 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 0 40 1 50 1 60 4 70 36 80 531 90 5274 95 1028 100 28 Following is the distribution of gaps Gaps # features -------- -------- 1000 4322 2000 1331 3000 657 4000 271 5000 110 6000 47 7000 35 8000 19 9000 15 10000 11 Following is the final summary # alignments : 6903 # unique Features these alignments represent: 6800 % of total features these alignments represent : 63.68 %