Entering edit mode
7.5 years ago
whaiyu06
▴
80
I have a file including about 10^6 different kinds of sequences,each of which is 20bp. Also,there is a library containing some 6000 different kinds sequences,20bp. I want to do a batch of pairwise global alignment to find the number of mismatch between the file and the library.So,someone will recommend a tool to handle this problem easily and fast?
So if I understood correctly you want to do 10^6 * 6000 pairwise alignments (~6 000 000 000) to get for each combination the amount of mismatches?
What are you working on? I'm not sure you are using the right approach to tackle this.
I just want to get the amount of mismatches or mismatches' distribution of each sequence in the file by global pairwise alignments,as you said.
What I want to do is to find how many sequences in the file (10^6) are from the library (6000),but bowtie just report the sequences less than 3 mismatches align with library. I want to know how differences between the sequences that failed to align and library.
Thanks for your answer!