Sequencing Vector Clip

Filename

sequence_vector_clip.p4m

Description

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).