Hello, I am fairly new to Biojava and I have recently encountered a problem concerning the results of the method pairwiseAlignment. It is my impression, and please do correct me if I am wrong, that the only results I can get from this class are: Time (ms): Length: Score: Query: query, Length: Target: target, Length: followed by the alignment itself.
What is more, this result is in a String format so I have to use some string manipulation methods in Java to extract each value, apart from the score which is the value returned from the call of the pairwiseAlignment method. However, what I am really interested in, is to find the percent identity of the two sequences. Therefore, I would be grateful to anyone that could point out a way to compute this percentage by using the data returned from the alignment. From what I have gathered by searching through the internet is that I need at least one of these: # of identical positions, # of aligned positions. Is it possible that the number of identical positions is the total number of " | " in the result of getAlignmentString()? Yeap, I am really confused. Some more information on my code: I am using the exact code presented in the Biojava Cookbook for global alignment with the NUC.4.4 substitution matrix. Thanks in advance, Katerina _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
