How to use
SEGID: An example
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SEGID: Conserved Segment Identification SEGID is a sequence analysis tool designed to identify conserved segments in a (multiple) sequence alignment. Conserved segments are high-scoring substrings in a long alignment which are probably biologically meaningful. SEGID accepts an alignment, converts the alignment into a sequence of numbers, one for each column, identifies its conserved segments, and generates graphical output. (It can also directly accept a sequence of numbers as input.) |
(Click the button on the left to start SEGID)
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SEGID provides three algorithms to identify 'interesting' segments: 1. Longest segment with average value lower bound; 2. All Maximal Length segments with average value lower bound and length lower bound; 3. N-Maximum Score Segments with length upper bound. (Click here to see formal definitions and algorithms.) SEGID has following advantages: # Focus on segments rather than individual columns; # Multiple adjustable parameters; # Fast calculation. All three algorithms run in linear time; # Compatible with multiple platforms; # User-friendly interface. |