Compressions and Stops

This option (which is available from the gap4 Experiments menu) searches through a region of a contig looking for stop (STOP) or compression (COMP) tags. These tags could have been added using the Contig Editor or by a suitable external program which can analyse traces to detect these types of problems. For each such tag found the routine produces a list of readings that could be resequenced to try to solve the problem. Obviously the types of experiments available will change as the technology improves but at present the program produces output that suggests "Taq terminator" experiments. We welcome suggestions for other experiment types or news of any programs that can automatically assign the tags. The results, in the form of suggestions, are written to the Output window.

Note that the Taq reading length is used as a guideline for deciding which readings are suitable candidates for solving a problem. All readings in the correct orientation and with their 5' ends within this length are assumed to solve the problem. The actual distance is listed in the output; an example of this is shown below.

  Prob 1544..1545: COMP tag on strand 0 (forward)
     Taq for xd26d8.s1          1365 179

  Prob 1554..1554: STOP tag on strand 0 (forward)
     Taq for xd26d8.s1          1365 189

  Prob 5276..5288: COMP tag on strand 1 (reverse)
     Taq for xc34g11.s1         5299  23
     Taq for xc34g11.s1t        5298  22
     Taq for xc34d6.s1          5316  40
     Taq for xc45e1.s1          5463 187

  Prob 24042..24046: COMP tag on strand 1 (reverse)
     Taq for xc50a12.s1        24167 125
     Taq for xc33d1.s1         24188 146
     Taq for xc36h4.s1         24208 166
     Taq for xc51c8.s1         24232 190

The format of the above output is:

  Prob <start>..<end>: <type> tag on strand <st>
      Taq for <read> @ <pos> <distance>
      ...

Where:

<start>..<end>

marks the inclusive range for the tag in the contig.

<type>

is the type of the current tag.

<st>

is the strand of the reading that the tag is placed upon

<read>

is the gel reading name.

<pos>

is the position of the 5' end of <read> in the contig.

<distance>

is the distance of the 5' end from the tag.