Dear Modellers,
When running the compare.log script on the TvLDH example
I obtained a qualitatively different aliignment than the "known"
which I downloaded from the web-site. Here is an excerpt
the compare.log file from the web-site , at line 442.
80 0.310 0.106 A 80 L 80 L 80 V 123
81 0.180 0.050 * D 81 D 81 D 81 D 124
82 0.212 0.039 Y 82 V 82 V 82 W 125
83 0.206 0.047 * A 83 A 83 A 83 A 126
84 0.165 0.073 L 84 I 84 I 84 L 127
85 0.122 0.037 * L 85 L 85 L 85 L 128
86 0.158 0.052 V 86 V 86 V 86 I 129
87 0.347 0.031 * G 87 G 87 G 87 G 130
88 0.609 0.174 A 88 S 88 S 88 A 131
# =============================================
89 1.375 0.314 P 90 M 89 M 89 P 133
# =============================================
90 1.479 0.649 R 97 L 100 D 99 R 140
# =============================================
91 1.463 0.278 V 103 A 103 A 103 I 146
92 0.782 0.226 * N 104 N 104 N 104 N 147
93 1.087 0.426 G 105 V 105 V 105 G 148
94 0.845 0.340 K 106 K 106 K 106 Q 149
95 0.411 0.068 * I 107 I 107 I 107 I 150
96 0.386 0.096 * F 108 F 108 F 108 F 151
97 0.542 0.245 T 109 K 109 K 109 A 152
98 0.478 0.214 E 110 C 110 C 110 D 153
99 0.216 0.029 * Q 111 Q 111 Q 111 Q 154
Here is the same region of the file from my own run:
80 0.312 0.109 A 80 L 80 L 80 V 123
81 0.185 0.053 * D 81 D 81 D 81 D 124
82 0.216 0.042 Y 82 V 82 V 82 W 125
83 0.209 0.049 * A 83 A 83 A 83 A 126
84 0.167 0.075 L 84 I 84 I 84 L 127
85 0.126 0.040 * L 85 L 85 L 85 L 128
86 0.163 0.054 V 86 V 86 V 86 I 129
87 0.349 0.027 * G 87 G 87 G 87 G 130
88 0.610 0.174 A 88 S 88 S 88 A 131
# =============================================
89 1.383 0.320 P 90 M 89 M 89 P 133
# =============================================
90 1.481 0.649 R 97 L 100 D 99 R 140
# =============================================
91 1.160 0.416 L 101 K 102 K 102 L 144
# =============================================
92 1.456 0.284 V 103 A 103 A 103 I 146
93 0.776 0.235 * N 104 N 104 N 104 N 147
94 1.083 0.431 G 105 V 105 V 105 G 148
95 0.840 0.344 K 106 K 106 K 106 Q 149
96 0.407 0.072 * I 107 I 107 I 107 I 150
97 0.380 0.101 * F 108 F 108 F 108 F 151
98 0.536 0.252 T 109 K 109 K 109 A 152
If I understand the output correctly the gap
structure of the alignments is different between the
two runs. I will be sending my directory contents under
separate cover. I would greatly appreciate your input
as to whether this discrepancy is due to
A. Numerical differences between running the program
on different machines.
B. A problem with the Version for the Alpha.
C. A problem with my installation of the Alpha Version.
D. An error on my part running the program.
Thanks and best wishes,
Rich
--------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
Department of Medical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
http://cancercenter.ccc.columbia.edu/~friedman/
In Memoriam, Robert Kanigher