This reports the protocol used to align the Maize_ArrayGene_NSF58K features to Maize_BACs_20060126. Mon Feb 13 19:41:52 2006 Source of Maize_ArrayGene_NSF58K : Downloaded from TIGR http://www.maizearray.org/files/remapping_version3_57452_fasta.zip Alignment procedure details --------------------------- 57452 Maize_ArrayGene_NSF58K are aligned to Maize_BACs_20060126 using blat with blat parameters -minScore=120 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'Coding-SameSpecies' data sets. Initial summary # alignments : 11644 # unique Features these alignments represent: 8309 % of total features these alignments represent : 14.46 % The following is the distribution of the feature coverage %coverage no of alignments -------- -------- 9 277 19 584 29 682 39 652 49 530 59 526 69 478 79 608 89 990 90 152 91 188 92 219 93 307 94 328 95 362 96 474 97 594 98 745 99 935 100 2013 Alignments less than 95 % coverage are deleted # remaining Alignments : 4786 # unique Features these remaining alignments represent: 3219 % of total features these alignments represent : 5.60 % Gap distribution of the remaining features Gaps # alignments -------- -------- 1000 3792 2000 409 3000 169 4000 88 5000 60 6000 16 7000 31 8000 29 9000 17 10000 20 20000 69 Alignments with gaps > 4000 bp are deleted # remaining Alignments : 4458 # unique Features these remaining alignments represent: 3012 % of total features these alignments represent : 5.24 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 0 91 0 92 0 93 0 94 31 95 131 96 252 97 508 98 815 99 1558 100 1163 Frequency distribution of the remaining features # hits # features -------- -------- 1 2366 2 413 3 95 4 36 5 28 6 21 8 30 9 6 10 1 20 12 30 3 40 0 50 1 100 0 Features that hit more than four times are deleted. # remaining Alignments : 3621 # unique Features these remaining alignments represent: 2910 % of total features these alignments represent : 5.07 %