The sequences can be very long. The program does a match of all sequence words of size 20 (by default). It then reduces this to the minimum set of overlapping matches by sorting the matches in order of size (largest size first) and then for each such match it removes any smaller matches that overlap. The result is a set of the longest ungapped alignments between the two sequences that do not overlap with each other. If the two sequences are identical in their region of overlap then there will be one region of match and no mismatches.
It should be possible to merge sequences that are Mega bytes long. Compare this with the program merger which does a more accurate alignment of more divergent sequences using the Needle and Wunsch algorithm but which uses much more memory.
The sequences should ideally be identical in their region of overlap. If there are any mismatches between the two sequences then megamerger will still attempt to create a merged sequence, but you should check that this is what you required.
A report of the actions of megamerger is written out. Any actions that require a choice between using regions of the two sequences where they have a mismatch is marked with the word WARNING!. The sequence in these regions is written out in uppercase. All other regions of the output sequence are written in lowercase.
Where there is a mismatch then the sequence that is chosen to supply the region of the mismatch in the final merged sequence is that sequence whose mismatch region is furthest from the start of end of the sequence.
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A merged sequence is written out.
Where there has been a mismatch between the two sequences, the merged sequence is written out in uppercase and the sequence whose mismatch region is furthest from the edges of the sequence is used in the merged sequence.
The name and description of the first input sequence is used for the name and description of the output sequence.
A report of the merger is written out.
Compare this with the program merger which does a more accurate alignment of more divergent sequences using the Needle and Wunsch algorithm but which uses much more memory.
A graphical dotplot of the matches used in this merge can be displayed using the program dotpath.