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Searching for point mutations using pregap4 and gap4

Edith Schlagenhauf ediths at botinst.unizh.ch
Mon Dec 1 08:40:49 EST 2003


we are looking for a point mutation in a bac.

Trying to process the data (for numerous different primer
pairs) using a simple text database as follows:

# BAC database 031121 ES, abi377 files from 031106
#ID         ST PR WT
1ATG1_11_Fa 2  1 1ATG1_col_F
1ATG1_11_Fb 2  1 1ATG1_col_F
1ATG1_11_Ra 2  2 1ATG1_col_R
1ATG1_col_F 2  1 1ATG1_col_F
1ATG1_col_R 2  2 1ATG1_col_R
1ATG2_11_Fb 2  1 1ATG2_col_F
1ATG2_11_Rb 2  2 1ATG2_col_R
1ATG2_col_F 2  1 1ATG2_col_F
1ATG2_col_R 2  2 1ATG2_col_R
1ATG3_11_Fa 2  1 1ATG3_col_F
1ATG3_11_Fb 2  1 1ATG3_col_F
1ATG3_11_Rb 2  2 1ATG3_col_R
1ATG3_col_F 2  1 1ATG3_col_F
1ATG3_col_R 2  2 1ATG3_col_R

always fails with error messages:

Tracediff: Insufficient sequence overlap to compute trace difference
for /home/ediths/Projects/BAC/BAC031106abi377/1ATG1_col_R.ztr.
Tracediff: Insufficient sequence overlap to compute trace difference
for /home/ediths/Projects/BAC/BAC031106abi377/1ATG1_11_Ra.ztr.

Processing the 3 batches of data, 1ATG1, 1ATG2, 1ATG3, separately
in the same way appears to work perfectly well.

Since I would like to process all the data in a single run, is there
any way to do this?

Thanks for your help,
Edith Schlagenhauf

N.B. is it possible to provide WL and WR info by way of a simple text
database at all?

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