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Directed Assembly

This assembly method assumes that a preprocessing program has been used to map the relative positions of the readings to within some level of accuracy or tolerance. The experiment file for each reading must contain a special "Assembly Position" or AP line that defines the position at which to assemble the reading. The position is not defined absolutely, but relative to any other reading (the "anchor reading") that has already been assembled. The definition includes the name of the anchor reading, the sense of the new reading, its offset relative to the anchor reading and the tolerance. i.e.:

AP   anchor_reading sense offset tolerance

The sense is defined using + or - symbols, the offset can be of any size and can be positive or negative. For normal use tolerance is a non-negative value, and the first base of the new reading must be aligned at plus or minus "tolerance" bases of "offset". If tolerance is zero, after alignment the position must be exactly "offset" relative to the anchor reading. If tolerance is negative then alignment is not performed and the reading is simply entered at position "offset" relative to the anchor reading. If the anchor reading is named *new* or is missing the reading starts a new contig and the other values on the AP line are not required.

Example AP line:

AP   fred.021 + 1002 40

The algorithm is as follows. Get the next reading name, read the AP line, find the anchor reading in the database, get the consensus for the region defined by anchor_reading + offset +/- tolerance. Perform an alignment with the new reading, check the position and the percentage mismatch. If OK enter the reading.

Obviously the way the positions of readings are specified is very flexible but one example of use would be to employ a file of file names containing a left-to-right ordered list of reading names, with each reading using the one to its left as its anchor reading. In this way whole contigs can be entered.

Although not specifically designed for the purpose this mode of assembly can be used for "assembly onto template". Also it can be used instead of "Enter preassembled data" if the tolerance is set to a negative value. See section Enter Pre-assembled data.

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If required, the alignments can be shown in the Output window by selecting "Display alignments". Only readings for which the "Maximum percent mismatch" after alignment is not exceeded will be entered into the database.

Assembly usually works on sets of reading names and they can be read from either a "file" or a "list" and an appropriate browser is available to enable users to choose the name of the file or list. If just a single reading is to be assembled choose "single" and enter the filename instead of the file or list of filenames.

The routine writes the names of all the readings that are not entered to a "file" or a "list" and an appropriate browser is available to enable users to choose the name of the file or list.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_22.html