How to align new DNA sequences with existing multiple DNA sequence alignment

Question

[liaoyunshi]

Many thanks for reading my post.

I want to align some short sequences into an existing multiple sequence alignment of long sequences. The short sequences are partial segments of the long sequences, about 1/10 in length.

I think under this situation I should use "profile alignment" strategy, and I do find some programs like MAFFT, Clustal, MUSCLE and T-COFFEE have this function. But I wonder if the short sequences would be aligned into the existing MSA fragmentarily due to the global alignment algorithm. However, in fact, the short sequences should locate intactly within some part of the existing MSA. So I think I should a local alignment program to conduct the profile alignment.

As far as I know, I would think all of MAFFT, Clustal, MUSCLE and T-COFFEE are global alignment tools. So I wonder if there is any local alignment program can conduct the profile alignment, or some of MAFFT, Clustal, MUSCLE and T-COFFEE do have incorporated local alignment algorithm.

Thanks.

[st.ph.n]

Clustal has an option for profile alignment:

 **************************************************************
 ******** CLUSTAL 2.1 Multiple Sequence Alignments  ********
 **************************************************************


     1. Sequence Input From Disc
     2. Multiple Alignments
     3. Profile / Structure Alignments
     4. Phylogenetic trees

     S. Execute a system command
     H. HELP
     X. EXIT (leave program)


Your choice: 3