GeneMachine ----------------------------- Instructions on installation are in the INSTALL file. Changes from past versions are in the CHANGES file. GeneMachine is a collection of Perl modules and a Perl program which will run GRAIL, MZEF, GENSCAN, HMMGene, FGENES, Sputnik, RepeatMasker and BLAST and print the output in ASN.1 format which is readable by NCBI's submission tool/Data Analysis WorkBench Sequin. This version requires that all the programs be installed on the machine in which GeneMachine is running; except for GRAIL which is run over the network. Sequin can be obtained from ftp://ncbi.nlm.nih.gov/sequin A custom configuration file for Sequin has been included in this distribution. See sequin_conf/README for instructions. A CGI program has been included in this distribution. This program supplies a frontend so users can plug their sequence(s) into a web page and have the sequin file mailed to them. See web_frontend/README for installation instructions DOCUMENTATION POD style documentation is included in the genemachine program. use the 'perldoc' utility to extract documentation from the genemachine directly. perldoc genemachine This should work if genemachine is in your path. The latest docs are always available at http://genome.nhgri.nih.gov/genemachine/ AVAILABILITY The latest version of GeneMachine should always be available from: ftp://ftp.nhgri.nih.gov/pub/software/genemachine/ PREREQUISITES In order to install and use this package you will need Perl version 5.004 or better. We recommend that you have the following packages installed before you install GeneMachine: For GENSCAN to work (optional) o GENSCAN - Chris Burge chris@CCR-081.mit.edu You must send mail to the author to obtain this program. Files ship as executables only. I know there are binaries for Solaris, IRIX6.x and Linux2.x. For HMMGene to work (optional) o HMMGene - Anders Krogh krogh@cbs.dtu.dk You must send mail to the author to obtain this program. Files ship as executables only. I know there are binaries for IRIX6.x and Linux2.x. For FGENES to work (optional) o FGENES - Victor Solovyev solovyev@sanger.ac.uk Victor Solovyev has left the Sanger Centre and development has been taken over by Softberry, Inc. (http://www.softberry.com/) For information on acquiring the package cantact softberry@softberry.com At the time of this writing an academic site license was $1000 USD. For MZEF to work (optional) o MZEF - Michael Zhang mzhang@cshl.org SunOS 5.5 and DEC Alpha executables are available from ftp://cshl.org/pub/science/mzhanglab/mzef/ There is also an IRIX6.x executable for the Human version. There are Linux executables for Arabadopsis and Human If you have a version of MZEF which accepts command line switches you will need to change the following line in the genemachine script from: use Mzef; to: use Mzef_cmd; o mzef.expect - Joseph Ryan jfryan@nhgri.nih.gov If you are using the interactive version of MZEF you will need the mzef.expect script which is available at: ftp://ftp.nhgri.nih.gov/pub/software/mzef.expect This is an expect script which allows you to run MZEF in a non-interactive way. It requires an Expect Interpreter. For Sputnik to work (optional) o Sputnik - Chris Abajian chris@abajian.com ftp://ftp.nhgri.nih.gov/pub/software/sputnik This program is available as C source code. For BLAST to work (optional) o NHGRI::Blastall - Joseph Ryan jfryan@nhgri.nih.gov VERSION 0.52 or later is required. To check version type perl -MNHGRI::Blastall -e 'print "$NHGRI::Blastall::VERSION\n";' ftp://ftp.nhgri.nih.gov/pub/software/blastall This is a Perl Module. o NCBI's Local BLAST (optional) ftp://ftp.ncbi.nlm.nih.gov/blast/executables/ Executables are available for DEC Alpha, Linux, SGI, Solaris, and Win32 For Help installing these executables see http://genome.nhgri.nih.gov/blastall/blast_install/ o nr, swissprot and est databases (optional) These databases must be installed for the default BLAST settings to work. The RAW databases are over 1.2 gigs (as of 5-14-99) The formated databases are over 1.5 gigs (as of 5-14-99) so you will probably need AT LEAST a 3 gig partition dedicated to these dbs ftp://ncbi.nlm.nih.gov/blast/swissprot.Z ftp://ncbi.nlm.nih.gov/blast/est.Z ftp://ncbi.nlm.nih.gov/blast/nt.Z (put a link from nt indexes to nr after running formatdb... ln -s nt.nhr nr.nhr ln -s nt.nin nr.nin ln -s nt.nnd nr.nnd ln -s nt.nni nr.nni ln -s nt.nsd nr.nsd ln -s nt.nsi nr.nsi ln -s nt.nsq nr.nsq For RepeatMasker to work (optional) o phrap/crossmatch/swap - Phil Green pg@umpqua.genome.washington.edu o RepeatMasker - Arian Smit asmit@u.washington.edu SUPPORT Questions about how to install and use WebBLAST should be directed to the genemachine@nhgri.nih.gov Bug reports and suggestions for improvements can be sent to genemachine@nhgri.nih.gov For more general information see the GeneMachine homepage: http://genome.nhgri.nih.gov/genemachine/ PUBLIC DOMAIN NOTICE This software/database is "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the authors' official duties for the United States Government and thus cannot be copyrighted. This software/database is freely available to the public for use without a copyright notice. Restrictions cannot be placed on its present or future use. Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the National Human Genome Research Institute (NHGRI) and the U.S. Government does not and cannot warrant the performance or results that may be obtained by using this software or data. NHGRI and the U.S. Government disclaims all warranties as to performance, merchantability or fitness for any particular purpose. In any work or product derived from this material, proper attribution of the authors as the source of the software or data should be made, using http://genome.nhgri.nih.gov/genemachine/ as the citation. --------------------------------------------------------------------------- Special thanks to Peter Kuehl of NCBI for his insight into ASN.1 and SEQUIN.