On 07/01/2009 05:33 AM, shilpi wrote: > I have aligned three homologous protein sequences by > salign_profile_profile.py , but the alignment file obtained is not > accurate. Can anyone tell me which script should I use for multiple > sequence alignment.

That is not surprising - profile-profile alignment aligns two blocks of previously-aligned sequences (two profiles). For example, salign_profile_profile.py in the Modeller examples/salign/ directory aligns two profiles read from mega_prune.faa; the first contains 15 sequences (align_block=15) and the second contains the remaining sequences from mega_prune.faa.

For multiple alignment, if you have structures, use salign_multiple.py or salign_iterative.py. If you only have sequences, either use malign or modify the salign parameters in your existing script - at a minimum you need to change align_what='BLOCK', alignment_type='TREE' and similarity_flag=False, and remove align_block.

Ben Webb, Modeller Caretaker