This module uses the
vector_clip program to identify and mark the
sequencing vector (those used to produce templates for sequencing, eg m13mp18
or puc18). To achieve this task it needs to know information about the vector
including the cut site position and the position of the primer site relative
to the cut site.See section Defining the Positions of Cloning and Primer Sites for Vector_Clip..
- Option: Use Vector-primer file
Vector_clip may be told to search through a series of vectors and primers held
within an external file. Alternatively we can request that it looks only at
one specific, known, vector. This question is to determine which of the two
mutually exclusive methods to use. In general it is still important for the
Experiment File to contain primer and template data. This module should not
(and cannot) be used to avoid doing that.
- Option: Vector-primer filename.
This is only used if the "Use Vector-primer file" question was answered with
"Yes". Each input sequence will be compared against each vector-primer pair to
find the best match. This provides a simple way of comparing against multiple
vectors or comparing against both forward and reverse primers of a single
vector. For further details on creating this vector-primer file, seesection Vector_Primer file format..
- Option: Vector file name
This, and the following two options, is only used if the "Use Vector-primer
file" question was answered with "No". The filename containing the vector
sequence. At present this should be a file containing a single plain text
sequence containing just the bases or white space.
- Option: Cut site
The cut site specified as a base count from the start of the vector file.
- Option: Primer site
The primer site specified as a base offset from the cut site. If two values
are specified separated by a slash, then this gives the values for the
universal forward and reverse primers (for example "
41/-24"). Use this
format only if the
PR (primer type) experiment file line type is known.
(This is the case when using the Sanger Centre naming conventions.) If the
primer site indicates a custom primer sequence then the primer site is taken
to be 0. Note that this will also happen if the primer site value is unknown.
- Option: Percentage minimum 5' match
- Option: Percentage minimum 3' match
Both ends of the sequence are checked using a dynamic programming algorithm to
find the optimal alignment. An end is marked as vector if the
percentage match is at least as high as this supplied parameter.
- Option: Default 5' position
This specifies the value to use for marking the 5' sequencing vector if none
is detected. Specifying this as -1 will cause the absolute value given for the
primer site (which is specified as relative to the cut site).
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Last generated on 2 Febuary 1999.