I am trying to find a region in Drosophila genome that is known in Bombyx.I tried using Pairwise global alignment in EMBOSS but the alignment is all wrong. I know it is wrong because parts of the Bombyx align too deep into the Drosophila genome,it should not be that far down. What can I do?
Do a local alignment of fragment from region of interest and genome. Direct alignment of whole genomes need specialized algorithm.
If interested in latter, use Mauve.
Search for your region using this genome database browser.
http://genome.ucsc.edu/cgi-bin/hgBlat
You can identify similar regions by using mummer tool.
Check the manual.
http://mummer.sourceforge.net/manual/
Personally i use ACT (ARTEMIS comparaison tool ) easy to use with graphical interface
https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act
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