This reports the protocol used to align the Maize_BACend features to tigrv4-genome. Fri Apr 14 17:08:53 2006 Source of Maize_BACend : from Gramene markers database, originally Downloaded from genbank with query '(txid4577[orgn] AND Wing[AUTH] AND Messing[AUTH] AND "BAC ends"[ALL])' Alignment procedure details --------------------------- 141928 Maize_BACend 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 : 64854 # unique Features these alignments represent: 43363 % of total features these alignments represent : 30.55 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 15641 150 6309 200 5709 250 5060 300 4416 350 4534 400 4622 450 4728 500 3381 550 2599 600 1506 650 1205 700 954 750 1208 800 637 10000 2345 Alignments with matches less than 100 bp are filtered # remaining Alignments : 49365 # unique Features these remaining alignments represent: 31931 % of total features these alignments represent : 22.50 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 46162 2000 38 3000 33 4000 15 5000 40 6000 14 7000 17 8000 13 9000 15 10000 7 20000 82 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 46248 # unique Features these remaining alignments represent: 29685 % of total features these alignments represent : 20.92 % Frequency distribution of the remaining features # hits # features -------- -------- 1 22531 2 3625 3 940 4 878 5 852 6 680 8 103 9 16 10 16 20 35 30 6 40 3 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 32601 # unique Features these remaining alignments represent: 27096 % of total features these alignments represent : 19.09 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 58 30 544 40 1276 50 1887 60 3684 70 10459 80 8180 90 4592 100 1921 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 25760 # unique Features these remaining alignments represent: 21269 % of total features these alignments represent : 14.99 % Following is the final summary # alignments : 25760 # unique Features these alignments represent: 21269 % of total features these alignments represent : 14.99 %