Hello, I have a bunch of DNA sequences (group A) I'm going to turn into a Stockholm MSA and I hope to use this to search another collection DNA sequences with nhmmer in HMMER to hopefully pick out anything that might be related to group A.
Problem 1: I was reading through the userfile and its not really clear what format the 'database' of DNA sequences needs to be in. Can I just put them together as a Stockholm MSA against a FASTA database?
Problem 2: Group A varies widely in length and content they are binding sites which I'm not even sure have directly similar sequences at all. When I try to input them into ClustalO to get a multiple sequence alignment I get an error.
ERROR: Cannot open input file. No alignment! Exit code: 255
Is there someway I can just generate the best alignment possible without having to worry about some threshold that will case my input to be outright rejected? Is there some alignments so bad Hmmer will just flat out reject them?