Dear All, Is there a way I can get individual alignments for a query sequence with the members of the HMM profile? Thanks in advance. Best Rajesh -- Ratna Rajesh Thangudu Research Scholar Laboratoire de Biochimie et Génétique Moléculaire Université de La Réunion 15 avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09 La Réunion, France Tel : +262 262 93 8641 Fax : +262 262 93 8237 Email : rajesh.thangudu at univ-reunion.fr ratnarajesh at yahoo.com