We are building a hybrid algorithm for the pairwise genome alignment. It will be validated with hypotetic constructed genomes.
Then we require a set of real genomes that will be of interest in the search for the optimal alignment
The best way is to validate using datasets from highly curacted genomic records, such as O. sativa, E. coli, M. tuberculosis and H. sapiens. Remember to try with genomes with different characteristics (high repetitive content, high or low GC content, many chromosomes, large genomes, SINE/LINE regions ...), as they may tricky your (and almost all) algorithm for genome alignment. Also try to validate using genomes with structural variations already validated (ex: Article Genome reduction in Leptospira borgpetersenii reflects limit...
).Are you going to compare your algorithm to MUMmer and LAST?
i dont know yet what algorithm for comparison. Mauve also seams to work with alignments.
anyway this algorithm is expected to perform pure alignment without those arrangements like reverse and translocation
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