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A tool for visualizing sequence alignments and associating annotations

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https://ir.library.oregonstate.edu/concern/graduate_projects/qr46r775s

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  • Alignment of genomic sequences from different species is becoming an increasingly powerful method in biology, and is being used for many purposes. The result of sequence alignments is a list of pairs of matched locations between the pattern string and the text string. However, without any proper visualization tools to help interpret the alignment result it's difficult for humans to read, not to mention analyze, the sequence alignment result. If the pattern string is small, it s easy to group the matches into regions manually. For large pattern strings. we need a method to automate the grouping process. In this paper a tool for visualizing sequence alignments and associating annotation is presented. In the visualizing sequence alignment part a grouping process called "alignment region clustering" is used to show the clustered regions of the alignment in 2D. Furthermore users can pick their own settings to cluster regions filter and visualize the result in almost linear time (assuming the input data is presorted, otherwise in O(N log N) time. In the associating annotation part, the tool matches a clustered region from an alignment with the closest region from GenBank's annotation(s) and allows users to save the matched result.
  • Keywords: alignment region clustering, annotation association
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