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.)
How to use SEGID: An example
(Click the button on the left to start SEGID)
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.