Dear Authors,

Thank you for nice work it is nice materials for fusion gene detection and analysis.

I have a few question for you.

1. EST dataset? It wold be greatly helpful if you publish your list of fused EST dataset as a supplementary material.

2. From the mRNA dataset, I prepared fasta files in order to align using newest version of BLAT & GMAP. I got consistent results for most of mRNA dataset. But I found some discrepancy for some of mRNA sequences. Maybe one of the fusion side is comprized of repeat sequences. For example, AF118081 mapped chr11:1975060-1982822 from 0 to 727, and chr19:41196814-41253812 from 484 to 1374. There are 243 bp overlap between two alignments which indicates AF118081 cannot meat your criteria for fused sequences.

Here are a few examples.

1919 39 0 0 10 24 10 171491 + BC040590 3038 1041 3023 17
78774742 2057649 2231098 21 18,16,3,24,9,8,1,3,4,4,6,7,21,17,5,28,103,470,168,253,790, 1041,1063,1081,1
084,1108,1117,1128,1132,1138,1142,1148,1154,1161,1185,1203,1209,1237,1342,1812,1980,2233, 2057649,2057667,2057683,
2057689,2057719,2188666,2188674,2188675,2188678,2188683,2188687,2190148,2190156,2190177,2190194,2190199,2227424,2227527,
2229079,2229475,2230308,
1346 13 0 0 0 0 1 21104 + BC040590 3038 0 1359 X
154913754 46935765 46958228 2 1238,121, 0,1238, 46935765,46958107,

869 16 0 0 2 5 4 56113 + AF118081 1374 484 1374 19
63811651 41196814 41253812 7 8,4,18,2,17,3,833, 484,492,499,519,521,538,541, 41196814
,41196825,41196829,41196847,41196850,41196870,41252979,
696 29 0 0 1 2 3 7037 + AF118081 1374 0 727 11
134452384 1975060 1982822 5 549,80,67,24,5, 0,549,629,698,722, 1975060,1982643,1982724,1982791,1982817,

1104 13 0 0 2 4 4 40420 + BC038772 1678 520 1641 8
146274826 49011736 49053273 7 8,26,41,13,16,118,895, 520,529,558,599,612,628,746, 49011736
,49011744,49011770,49032705,49032719,49052258,49052378,
753 26 0 0 2 5 7 84862 + BC038772 1678 0 784 18
76117153 32663075 32748716 10 82,36,143,95,274,109,8,19,10,3, 0,82,118,261,356,630,739,747,768
,781, 32663075,32668280,32669194,32678168,32719517,32748562,32748673,32748684,32748703,32748713,

1622 33 0 0 1 3 4 15860 - AK126172 2253 0 1658 22
49691432 28546627 28564142 6 33,13,100,53,747,709, 595,628,641,744,797,1544, 28546627
,28546661,28549587,28549687,28562685,28563433,
919 25 0 0 0 0 4 36360 + AK126172 2253 1309 2253 6
170899992 41640795 41678099 5 117,7,13,10,797, 1309,1426,1433,1446,1456, 41640795
,41640918,41640926,41677290,41677302,

1129 11 0 0 0 0 3 23630 - BC047770 1902 743 1883 17
78774742 2266090 2290860 4 1033,63,1,43, 19,1052,1115,1116, 2266090,2267128,2267194,2290817,
861 19 0 0 2 2 2 945 + BC047770 1902 0 882 1
247249719 9217519 9219344 5 788,1,16,38,37, 0,788,790,806,845, 9217519,9219250,9219251,9219269,9219307,

371 10 0 0 2 4 2 2274 - AF085869 567 0 385 2
242951149 11329311 11331966 5 7,49,55,1,269, 182,190,239,297,298, 11329311,11329318,113302
19,11330274,11331697,
300 1 0 0 0 0 0 0 + AF085869 567 266 567 4
191273063 71951264 71951565 1 301, 266, 71951264,

1183 1 0 0 0 0 0 0 - AK094335 1882 0 1184 13
114142980 51902085 51903269 1 1184, 698, 51902085,
1234 169 0 0 22 47 27 154486 - AK094335 1882 432 1882 2
242951149 71268945 71424834 49 228,177,149,144,4,7,6,2,8,8,10,10,8,10,14,2,5,10,10,10,8,2,3,21,
23,21,5,28,4,11,5,11,12,4,2,12,8,22,6,17,7,4,40,262,4,4,16,6,13, 0,228,405,554,698,707,716,722,724,732,740,751,76
3,771,781,796,799,804,816,827,837,846,851,854,875,901,922,927,958,963,974,979,990,1002,1006,1013,1026,1034,1058,1064,108
1,1088,1095,1136,1400,1406,1414,1430,1437, 71268945,71270482,71283089,71307565,71308198,71308202,71308209,71308218,
71308221,71308232,71311323,71311333,71311343,71312993,71313007,71313021,71313023,71313031,71313041,71313051,71352698,713
52706,71352708,71380846,71380870,71380893,71380917,71380923,71380951,71380955,71380969,71408653,71409495,71409509,714099
67,71409969,71409981,71410523,71410545,71410553,71410573,71416719,71416723,71424523,71424785,71424789,71424793,71424815,
71424821,

1242 9 0 0 1 1 2 1156 + AB073889 2091 839 2091 10
135374737 104513786 104516193 4 16,1198,25,12, 839,856,2054,2079, 104513786,104513802,1045
16154,104516181,
913 13 0 0 0 0 1 9498 + AB073889 2091 0 926 8
146274826 32279120 32289544 2 859,67, 0,859, 32279120,32289477,

2394 4 0 0 0 0 18 50354 - Z22957 4281 2 2400 15 10033891
5 50409928 50462680 19 60,94,199,101,9,228,54,144,114,149,94,249,240,81,73,212,109,87,101,
1881,1941,2035,2234,2335,2344,2572,2626,2770,2884,3033,3127,3376,3616,3697,3770,3982,4091,4178, 50409928,50415951,504196
84,50425849,50428306,50430742,50433093,50433359,50439456,50444042,50446519,50449657,50451612,50454792,50454876,50455835,
50459113,50459310,50462579,
1811 5 0 0 1 1 0 0 - Z22957 4281 2463 4280 14 10636858
5 79208346 79210162 2 932,884, 1,934, 79208346,79209278,


1993 0 0 0 0 0 11 8523 + AK096600 2827 834 2827 1
247249719 149766074 149776590 12 133,210,207,258,171,162,90,84,119,109,164,286, 834,967,1177,138
4,1642,1813,1975,2065,2149,2268,2377,2541, 149766074,149768449,149769008,149769588,149771501,149773074,149774141,14
9774699,149774879,149775336,149775829,149776304,
845 21 0 0 5 13 6 3593 - AK096600 2827 0 879 19
63811651 2667902 2672361 12 10,33,1,10,2,10,6,6,3,8,717,60, 1948,1958,1994,1998,2008,2010,2022,2030,2039,204
2,2050,2767, 2667902,2667913,2667946,2667947,2668115,2668118,2668128,2668134,2668140,2668145,2668156,2672301,