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Is this a bug?



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