Each cluster consists of overlapping fragments that could be chained together into a single, continuous assembly. It also gives the orientation of each sequence. WordSearch uses the same comparison algorithm as Overlap . WordSearch , however, accepts a single query sequence as input and finds regions of similarity rather than overlaps. GelOverlap is Overlap , customized to run in the fragment assembly environment.
LineUp is a screen editor for editing and displaying overlapping sequences.
The total length of bases in any sequence set may not exceed 350,000. No sequence in the query set may exceed 30,000 bases. The word size must be between 1 and 30. The minimum overlap length must be between 1 and 1,000. The program cannot store more than 10,000 overlaps.