Comparing two sets of 16s sequences to identify any identicle (within 97%) sequences

Question

[robert.murphy]

I have two sets of 16s sequences and want to see if there are any sequences within 97% similarity. Blastn uses local alignment and I am looking for global alignment (I think? please correct me on this). If I am indeed looking for global alignment what is an appropriate took to use that will return a % similarity score between the two sequeces?

[Joe]

Are you looking for similarities between the files or within the files too? My initial thought was simple to cluster everything at 97% identity with e.g. CD-HIT, and then investigate the clusters.

[robert.murphy]

I am looking between files :) I will give CD-HIT a look.

Answer 1

[Mensur Dlakic]

At that level of sequence identity local and global alignments are likely to be the same. You can test it by aligning two sequence using BLASTn or Needleman-Wunsch's global algorithm.