This reports the protocol used to align the Barley_ESTcluster_PlantGDB features to tigrv4-genome. Mon Apr 24 16:36:42 2006 Source of Barley_ESTcluster_PlantGDB : this is a set of EST clusters and singletons from Gramene markers database, originally down loaded from PlantGDB website.\nhttp://www.plantgdb.org/download/Download/Sequence/ESTcontig/Hordeum_vulgare/Hordeum_vulgare.PUT.fasta.bz2 Alignment procedure details --------------------------- 99915 Barley_ESTcluster_PlantGDB 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 : 63452 # unique Features these alignments represent: 58710 % of total features these alignments represent : 58.76 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 7226 150 7029 200 7458 250 7416 300 7051 350 6191 400 5245 450 4293 500 2922 550 2091 600 1493 650 1058 700 809 750 581 800 461 10000 2128 Alignments with matches less than 150 bp are deleted # remaining Alignments : 49340 # unique Features these remaining alignments represent: 45477 % of total features these alignments represent : 45.52 % Frequency distribution of the remaining features # hits # features -------- -------- 1 43682 2 1102 3 242 4 142 5 75 6 54 8 141 9 32 10 4 20 3 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 46612 # unique Features these remaining alignments represent: 45026 % of total features these alignments represent : 45.06 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 0 40 8 50 17 60 98 70 379 80 3862 90 31866 95 9779 100 603 Following is the distribution of gaps Gaps # features -------- -------- 1000 35688 2000 6183 3000 2128 4000 831 5000 336 6000 156 7000 141 8000 73 9000 58 10000 45 Following is the final summary # alignments : 46612 # unique Features these alignments represent: 45026 % of total features these alignments represent : 45.06 %