This reports the protocol used to align the Maize_Marker features to tigrv4-genome. Fri Apr 14 11:53:45 2006 Source of Maize_Marker : From the link http://www.agron.missouri.edu/files_dl/SequenceMap/SequenceMap20030425.txt, unique genbank accessions were pulled out and sequences were extracted from batch entrez Alignment procedure details --------------------------- 6970 Maize_Marker 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 : 4537 # unique Features these alignments represent: 3819 % of total features these alignments represent : 54.79 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 628 150 565 200 649 250 539 300 424 350 375 400 377 450 171 500 118 550 86 600 64 650 34 700 20 750 44 800 27 10000 415 Alignments with matches less than 150 bp are deleted # remaining Alignments : 3360 # unique Features these remaining alignments represent: 2768 % of total features these alignments represent : 39.71 % Frequency distribution of the remaining features # hits # features -------- -------- 1 2296 2 420 3 15 4 15 5 13 6 9 8 0 9 0 10 0 20 0 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 3181 # unique Features these remaining alignments represent: 2731 % of total features these alignments represent : 39.18 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 0 40 1 50 2 60 2 70 25 80 204 90 2094 95 650 100 203 Following is the distribution of gaps Gaps # features -------- -------- 1000 2390 2000 385 3000 191 4000 76 5000 27 6000 28 7000 9 8000 10 9000 5 10000 8 Following is the final summary # alignments : 3181 # unique Features these alignments represent: 2731 % of total features these alignments represent : 39.18 %