profgen generates various profiles for each alignment in a directory.

This is part of Jon Ison's protein structure analysis package. This package is still being developed. Please ignore this program until further details can be documented. All further queries should go to Jon Ison (

Here is a sample session with profgen:

% profgen

Mandatory qualifiers (bold if not always prompted):

-infpath (string)

Location of sequence alignment files (input).

-infextn (string)

Extension of sequence alignment files.

-type (menu)

Select type.

-threshold (integer)

Enter threshold reporting percentage.

-datafile (matrixf)

Scoring matrix.

-open (float)

Gap opening penalty.

-extension (float)

Gap extension penalty.

-smpfpath (string)

Location of simple profile files (output).

-smpfextn (string)

Extension of simple profile files.

-gbpfpath (string)

Location of Gribskov profile files (output).

-gbpfextn (string)

Extension of Gribskov profile files.

-hnpfpath (string)

Location of Henikoff profile files (output).

-hnpfextn (string)

Extension of Henikoff profile files.

Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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