This reports the protocol used to align the Maize_HiCot_Bennetzen features to tigrv4-genome. Fri Apr 14 18:27:37 2006 Source of Maize_HiCot_Bennetzen : Downloaded from Genbank with query '(txid4577[ORGN] AND Bennetzen[AUTH] AND Cot[ALL])' Alignment procedure details --------------------------- 446926 Maize_HiCot_Bennetzen 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-Genomic' data sets. Initial summary # alignments : 128256 # unique Features these alignments represent: 115753 % of total features these alignments represent : 25.90 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 42889 150 20604 200 16448 250 12630 300 9308 350 7217 400 5217 450 3937 500 2824 550 2034 600 1469 650 1088 700 755 750 652 800 578 10000 606 Alignments with matches less than 100 bp are filtered # remaining Alignments : 85846 # unique Features these remaining alignments represent: 79048 % of total features these alignments represent : 17.69 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 83532 2000 396 3000 100 4000 72 5000 85 6000 74 7000 55 8000 58 9000 33 10000 35 20000 242 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 84100 # unique Features these remaining alignments represent: 77534 % of total features these alignments represent : 17.35 % Frequency distribution of the remaining features # hits # features -------- -------- 1 74149 2 2207 3 418 4 273 5 234 6 102 8 67 9 26 10 30 20 26 30 1 40 1 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 79817 # unique Features these remaining alignments represent: 76774 % of total features these alignments represent : 17.18 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 10 30 95 40 409 50 954 60 1818 70 3470 80 10468 90 47282 100 15311 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 76749 # unique Features these remaining alignments represent: 73965 % of total features these alignments represent : 16.55 % Following is the final summary # alignments : 76749 # unique Features these alignments represent: 73965 % of total features these alignments represent : 16.55 %