Global Alignment using a FASTA type algorithm

[William R. Pearson]

In article <9607091945.AA03380 at notes.ncgr.org> Gautam_Singh/NCGR at NOTES.NCGR.ORG (Gautam Singh/NCGR) writes:

   Hi all:

   The current form of FASTA finds regions of local similarity between
   two sequences. Is there a similar program (c/c++ function) that
   computes the global alignment using the FASTA
   algoritm. Essentially, I would like to get a SIM (Huang, et. al.)
   type complete alignment from a program that uses FASTA ( or its
   derivitive) as its core alignment engine.

SIM also calculates local alignments. It is used in the "lalign" part of
the FASTA package.  The current linear-space algorithms that I know of
for calculating local alignments actually simply find the boundaries of
the local alignment and then do a global alignment in that region. Thus,
they all include linear-space global alignment code.  You simply need
to set the ends of the global alignment region to the ends of the sequences
to get global alignment.

Bill Pearson