We are pleased to announce that two additional assembly engines are
now available for use with gap4. These are CAP2 by Xiaoqui Huang and
FAKII by Eugene W Myers Jr., Mudita Jain, Eric Anson and Susan Larson.
We apologise if you have already seen this post.
Obtaining CAP2 for use with gap4
The CAP2 files for use with gap4 must be obtained via ftp from the
author, Xiaoqui Huang.
Email Xiaoqui Huang (huang at cs.mtu.edu) stating that you want CAP2 for
use with gap4 and the operating system for which you need the program
(one of: SunOS 4.1.1; Solaris 2.5; DEC OSF/1 V3.0 and Digital Unix;
Irix 5.3). He will then contact you to arrange for the retrieval of
the binary file. The binary file is called cap2_s. Make this
executable (eg chmod a+x cap2_s) and move it to the directory
$STADENROOT/bin. The CAP2 options on the assembly menu should now be
Obtaining FAKII for use with gap4
The FAKII files for use with gap4 must be obtained via ftp from the
authors Eugene W Myers Jr., Mudita Jain, Eric Anson and Susan Larson
at the University of Arizona, Department of Computer Science.
First email a request for authorization to Dr Gene Myers
(gene at cs.arizona.edu) stating you want FAKII for use with gap4. He
will email you a postscript file containing the authorization
document. Print the document. Read it. Sign it, fax it back to Gene
Myers at +1 (520) 621-4246 and also post the original signed copy back
Then email Susan Larson (slarson at cs.arizona.edu) requesting a copy of
FAKII for use with gap4 and she will contact you to arrange for the
transfer. Make sure you tell Susan the operating system for which you
need the program (one of: SunOS 4.1.1; Solaris 2.5; DEC OSF/1 V3.0 and
Digital Unix; Irix 5.3). Make the files Susan sends executable (eg
chmod a+x *) and move them into the directory $STADENROOT/bin. The
environment variable FAKII must also be set to $STADENROOT/bin, for
example, for the bash shell, export FAKII=$STADENROOT/bin. You could
add this to your staden.profile or staden.login files.
Prior to the files being in this directory the FAKII items on the
assembly menu in gap4 will have been greyed out; now they should
appear in normal text and the functions will be selectable.
For help on either CAP2 or FAKII, read the online documentation
available via gap4. Further information about gap4, CAP2 and FAKII can
be obtained from http://www.mrc-lmb.cam.ac.uk/pubseq/
Kathryn Beal, James Bonfield and Rodger Staden
Dr Kathryn Beal
Structural Studies, Lab Mol Biol, MRC, Hills Rd, Cambridge, CB2 2QH, UK
Phone 01223 402266