This reports the protocol used to align the RiceJaponica_cDNA_KOME features to Maize_BACs_20060126. Mon Feb 13 13:46:02 2006 Source of RiceJaponica_cDNA_KOME : Downloaded from Genbank with query 'FLI_CDNA[Keyword] AND Oryza[Organism] AND Kikuchi[Author]' Alignment procedure details --------------------------- 32127 RiceJaponica_cDNA_KOME are aligned to Maize_BACs_20060126 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 : 6731 # unique Features these alignments represent: 5732 % of total features these alignments represent : 17.84 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 1643 150 794 200 618 250 464 300 406 350 318 400 263 450 225 500 260 550 160 600 139 650 147 700 148 750 123 800 105 10000 918 Alignments with matches less than 150 bp are deleted # remaining Alignments : 4306 # unique Features these remaining alignments represent: 3655 % of total features these alignments represent : 11.38 % Frequency distribution of the remaining features # hits # features -------- -------- 1 3363 2 178 3 18 4 14 5 41 6 23 8 18 9 0 10 0 20 0 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 3773 # unique Features these remaining alignments represent: 3559 % of total features these alignments represent : 11.08 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 4 40 4 50 27 60 54 70 179 80 666 90 2330 95 393 100 116 Following is the distribution of Gaps Gaps # features -------- -------- 1000 2641 2000 446 3000 263 4000 145 5000 55 6000 33 7000 22 8000 36 9000 16 10000 13 Following is the final summary # alignments : 3773 # unique Features these alignments represent: 3559 % of total features these alignments represent : 11.08 %