Installing Windows NT Version of ProteinProspector (Intel processors only)

1. If you wish to access the programs over an intranet you'll need to have a service such as TCP/IP set up with Domain Name Service (DNS) and running through the Network control panel. If so you should learn the fully qualified name of your computer (something like yourcomputer.yourinstitution.com). Network access also facilitates moving sequence databases onto your computer. In order to run the programs directly from a single computer, however, network access is not necessary.

2. If your machine is not already configured as an http server, create a directory (eg. D:\http) to locate the software. Make sure you have enough disk space for your databases.

   As of Jan 15th 1999 the uncompressed sizes of the public FASTA databases supported by ProteinProspector were:

   • dbEST 1033 MB
   • Genpept 136 MB
   • NCBInr 147.5 MB
   • Owl 110 MB
   • SwissProt 34 MB

   By Sep 27th 2000 the corresponding database sizes were as follows:

   • dbEST full, 837 MB compressed, estimated 2.79 GBytes uncompressed
   • dbEST human, 352 MB compressed, estimated 1.17 GBytes uncompressed
   • dbEST mouse, 215 MB compressed, estimated 717 MBytes uncompressed
   • dbEST others, 268 MB compressed, estimated 893 MBytes uncompressed
   • Genpept 98.8 MB compressed, 236 MB uncompressed
   • NCBInr 135MB compressed, 256 MB uncompressed
   • Owl 65.2 MB compressed, 124 MB uncompressed - last updated May 22nd 1999
   • SwissProt 21.9 MB compressed, 39 MB uncompressed
   • Ludwignr 228 MB all elements uncompressed

   The sizes of the individual elements of the Ludwignr database were as follows:

   • gp_nr.seq 20.0 MB
   • gpu_nr.seq 1.90 MB
   • pir1_nr.seq 959 KB
   • pir2_nr.seq 5.40 MB
   • pir3_nr.seq 6.66 KB
   • pir4_nr.seq 37.2 KB
   • swiss_nr.seq 41.7 MB
   • swiss_varsplic_nr.seq 1.41 MB
   • trembl_new_nr.seq 40.2 MB
   • trembl_nr.seq 115 MB
   • trembl_varsplic_nr.seq 378 KB
   • wormpep_nr.seq 245 KB
   • yeastpep_nr.seq 140 KB

   In addition to this the files made by the FA-Index program are between 8-16% of the size of the database.

3. Place the Prospector distribution file (file name below) precompiled for your system to the D:\http directory.
   • Windows NT 3.51 and higher: prospector__nti.zip.

4. If you are upgrading from a previous ProteinProspector version this step may result in the results_msfit, results_mstag, results_msseq or results_mspattern directory from your previous version being overwritten. If you have saved any files in this directory you may wish to move them first. Otherwise version can coexist with previous versions on the same system as long as you use different names for the databases. All database index files need to be remade to run this release

   Unzip the Prospector distribution file so that directory structures are preserved, and that filenames longer than 8.3 are allowed. If double clicking on the file doesn't launch an unzipping tool on your computer, then download Winzip. . Check the box for "Use folder names" when extracting to preserve directory structures.
   You should then find the following:

   • mshome.htm
   • Readme.txt
   • results_mspattern
   • results_msfit
   • results_msseq
   • results_mstag
   • • gifs
     • instruct
     • js
     • misc

   The list above describes the suggested directory structure - once installation is complete - specifically designed for use with Microsoft Peer Web Services or Microsoft Internet Server.

   Special note on directory structure: the \ms*.cgi programs issue relative path requests for \, seqdb\, results_msfit\, results_mstag\, result_msseq\ and results_mspattern\ files. For Microsoft Peer Web Services the request is relative to the home directory specified in the Internet Service Manager (D:\http). For other http servers this request is likely to be relative to the ms*.cgi files, in which case these 5 directories should be located below the directory.

5. If your machine is already configured as a web server, skip to the next step. If your machine is not already configured as an http server, do so by following the instructions below. This will probably be the most time consuming part of the installation.
   • For Windows NT 4.0 configure TCP/IP and Microsoft Peer Web Services.
     • Contact your local network administrator to set up TCP/IP, then continue below with Microsoft Peer Web Services set up. Requires Administrator access privileges.
     • Open the Network Control Panel.
     • Select the Services tab.
     • If Microsoft Peer Web Services does not appear, click add and install from the Windows NT 4.0 system CD.
     • Close the Network control panel.
     • Start the Internet Services Manager (from the start menu, it should be under Programs -> Microsoft Peer Web Services (Common).
     • Double-click the WWW services feature, then click the directories tab.
     • Set the home directory as D:\http.
     • Enable the default document as mshome.htm if you want the ProteinProspector main page as the home page for your machine.
     • Optionally you may add the directory D:\http\. If you do this, make sure to click on execute privileges for this directory.

6. If you have a network service like TCP/IP running - and you left the http server configured to port 80 - you should now be able to point your web browser to http://yourcomputer.yourinstitution.com and retrieve the Prospector home page if the http server is setup correctly. Without TCP/IP running the web browser should be pointed to D:\http\mshome.htm (this can be done even if the http server is not running). The programs cannot be run unless the http server is running. Verify that the server and programs are working by pointing your web browser to http://yourcomputer.yourinstitution.com//msprod.htm, http://yourcomputer.yourinstitution.com//mscomp.htm or http://yourcomputer.yourinstitution.com//msiso.htm and clicking Induce Fragmentation. The other programs will not work until a database is installed. You must address the programs via an http:// type URL to provide the CGI syntax that invokes the executable. If you address a program via a URL of the form D:\http\\msprod.htm clicking submit will produce a save as dialog box because the http server is being bypassed.

7. Create the directory D:\http\seqdb, then install some databases and create the accompanying index files. If you wish to locate the databases in a directory on a separate drive from the rest of the ProteinProsepctor files, you may do so after editing the file D:\http\\js\info.js and providing a new path name for the variable: seqdbDir. You should not locate the databases on a drive located on a remote computer. Searches will be very slow because of network access time to read the database files.

8. This completes the installation. TIME TO TEST DRIVE. Access one of the input forms either from the links on the Prospector home page homepage or at the URL: http://yourcomputer.yourinstitution.com//msfit.htm and press the submit search input button. If you haven't been able to install the databases, the MS-Product, MS-Comp and MS-Isotope programs will still work, enabling you to test that you've installed everything correctly.

9. Try saving the results of a search to a file and then doing a search based on the saved results. If this doesn't work the folders results_msfit, results_mstag, results_msseq or results_mspattern and their contents need their file permissions changed to "Change (RWXD)". To set this option right click on the folder and select properties. Then choose the security tab, click on the permissions button, select the IUSR account (computername\IUSR_SOMENAME) and set the type of access to change.

10. After everything is running smoothly you might want to change the computer optimisation parameters to see if they have any effect on search times.