This reports the protocol used to align the Barley_ESTcluster_TIGR features to tigrv4-genome. Fri Apr 14 12:00:47 2006 Source of Barley_ESTcluster_TIGR : from Gramene markers database, originally Downloaded from TIGR from the link ftp://ftp.tigr.org/pub/data/tgi/Hordeum_vulgare/HVGI.release_9.zip Alignment procedure details --------------------------- 46352 Barley_ESTcluster_TIGR 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 : 36508 # unique Features these alignments represent: 17247 % of total features these alignments represent : 37.21 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 2358 150 2370 200 3006 250 2788 300 3002 350 2872 400 2754 450 2522 500 2152 550 1916 600 1460 650 1320 700 1094 750 998 800 854 10000 5042 Alignments with matches less than 150 bp are deleted # remaining Alignments : 31826 # unique Features these remaining alignments represent: 15037 % of total features these alignments represent : 32.44 % Frequency distribution of the remaining features # hits # features -------- -------- 1 0 2 14620 3 0 4 256 5 0 6 51 8 25 9 0 10 30 20 54 30 1 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 29240 # unique Features these remaining alignments represent: 14620 % of total features these alignments represent : 31.54 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 0 40 4 50 12 60 54 70 222 80 2450 90 21510 95 4816 100 172 Following is the distribution of gaps Gaps # features -------- -------- 1000 17878 2000 5612 3000 2804 4000 1226 5000 532 6000 210 7000 144 8000 96 9000 64 10000 42 Following is the final summary # alignments : 29240 # unique Features these alignments represent: 14620 % of total features these alignments represent : 31.54 %