a2m to selex Alignement Format Conversion Script
is for the building of HMMER models from high quality alignments in the 'a2m' format commonly used by SAM.
These files are the product of the T99 script for model-building
which produces excellent alignments with the match and insert states specified in upper and lower case
characters. Unfortunately this information is not used by HMMER. To use this information convert the SAM
'a2m' format to 'selex' format using the script (download at top of page). Run the HMMER 'hmmbuild' program
(version 2.1.1) with the '--hand' option and the states specified in the selex file extracted from the
alignment will be used instead of the states generated by HMMER by default.
Only use this procedure on alignments which you believe to have very well
specified aligned regions in upper case versus unaligned regions in lower case. The SAM T99 script produces
these, but hand alignments based on structural information may be another possible source.
N.B. The SAM program 'prettyalign' is a necessary
dependancy for this script and the path to the binary will need to be specified in the parameters at the top
of the script unless it is in your path.