Alignments provide a view of biological homology in two sequences. A new local alignment tool for protein sequences is presented here and it allows a single gap extended up to as long as user's request. After that, Neutral Area analyzes the query sequence to locate the segments of significant scores based on the found local alignments.
The local convergence shows regions of high-density occurrences on short motifs in a sequence. My study contains the details, examples and executables for both DNA and protein sequences.
The region of low complexity is defined to the biased composition of short patterns. This region may be gathered by several windows, which is a basic observation to measure the biased merit.
Last update: 12/11/2003