Hi I am a biologist not a bioinformatician, I have two group of sequences (they are nucleotide and in fasta format), each group includes around 40,000 sequences ranging from 100 bp to 12 kb. I want to know how can I align the sequences from a group to the another and find the best pair for each fragment. How can I do that? is there any softwares that can I use? second Q how can I find secondary structures of the sequences in each groups? which program should I use? Thanks MS
about the alignment part i hope that you can clarify it more
What I want to do is aligning each fragment (sequence) in one group against another group and only find the best pair for that one it continues for all fragments