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Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 2 15:45:45 2006 UTC (14 years ago) by hwang
Branch: MAIN
CVS Tags: HEAD
Changes since 1.21: +7 -5 lines
Diff to previous 1.21
Fixed broken links. Separated the tag from the link so there won't be broken links in the future.

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 17 20:49:24 2006 UTC (14 years ago) by hwang
Branch: MAIN
Changes since 1.20: +2 -2 lines
Diff to previous 1.20
The output of the data is not correctly formatted for ShowPage. This program needs to be altered.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 16 19:06:36 2006 UTC (14 years ago) by hwang
Branch: MAIN
Changes since 1.19: +12 -6 lines
Diff to previous 1.19
Files were changed to separate the links from the text. Links need to be separated because links are out of date after awhile.
The saved text in drug_targets.pl is in a format recognized by ShowTable.pl

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 4 03:10:09 2006 UTC (14 years, 4 months ago) by hwang
Branch: MAIN
Changes since 1.18: +2 -2 lines
Diff to previous 1.18
ShowTable.pl:
-took out underscore, improve download feature, improve layouts, sort by author enabled, link to subsystem
ShowTableKey.pl
-improve column description
drug_targets.pl
-link to current list

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 12 04:13:00 2005 UTC (14 years, 8 months ago) by hwang
Branch: MAIN
Changes since 1.17: +17 -6 lines
Diff to previous 1.17
ShowTable.pl - added a subroutine to delete old temporarily files
best_pdb.pl, drug_targets.pl, ShowTable.pl - The temporarily files were not created in consistant places. Changed all
    temporary files to be created in the Fig_Config::Tmp directory

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 2 19:44:35 2005 UTC (14 years, 9 months ago) by fangfang
Branch: MAIN
Changes since 1.16: +11 -9 lines
Diff to previous 1.16
Added augmented PDB links generated by PASS.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 2 02:05:06 2005 UTC (14 years, 9 months ago) by hwang
Branch: MAIN
Changes since 1.15: +23 -5 lines
Diff to previous 1.15
Added a button to allow user to save customized query to the master list. The master list can be view
by ShowTable.cgi

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 31 20:30:12 2005 UTC (14 years, 9 months ago) by hwang
Branch: MAIN
Changes since 1.14: +5 -3 lines
Diff to previous 1.14
Changed paths so it is not absolute and check to see if path exists.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 31 15:31:29 2005 UTC (14 years, 9 months ago) by hwang
Branch: MAIN
Changes since 1.13: +6 -12 lines
Diff to previous 1.13
Changed files to incorporate fangfang's and kaitlyn's script.
ShowTable.pl
	Shows and edits the tables in the archives

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 26 16:58:56 2005 UTC (14 years, 9 months ago) by fangfang
Branch: MAIN
Changes since 1.12: +24 -17 lines
Diff to previous 1.12
Added 'use strict;' and modified codes accordingly.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 25 23:22:54 2005 UTC (14 years, 9 months ago) by fangfang
Branch: MAIN
Changes since 1.11: +8 -8 lines
Diff to previous 1.11
Fixed the conservation script bug thanks to Bob.
Added category codes instructions page.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 24 17:56:09 2005 UTC (14 years, 9 months ago) by fangfang
Branch: MAIN
Changes since 1.10: +2 -3 lines
Diff to previous 1.10
Took out the border of Google Group box to make it neater.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 24 16:52:11 2005 UTC (14 years, 9 months ago) by fangfang
Branch: MAIN
Changes since 1.9: +33 -5 lines
Diff to previous 1.9
Attached Google Group promo boxes.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 23 04:30:13 2005 UTC (14 years, 9 months ago) by fangfang
Branch: MAIN
Changes since 1.8: +6 -1 lines
Diff to previous 1.8
Fixed a bug in Makefile

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 23 03:38:35 2005 UTC (14 years, 9 months ago) by fangfang
Branch: MAIN
Changes since 1.7: +1 -1 lines
Diff to previous 1.7
Enabled "Conservation" column calculation.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 23 03:32:58 2005 UTC (14 years, 9 months ago) by fangfang
Branch: MAIN
Changes since 1.6: +1 -1 lines
Diff to previous 1.6
Added new algorithm for computing degree of sequence conservation.

The algorithm looks for the homologs of one peg in 10 fixed organisms,
and uses clustalw to align the 10 sequences. Conservation value is then
calculated based on the aligned fasta file.

The algorithm decides which 10 organisms to compare based on whether
this peg belongs to a gram positive bacteria or not.

cons_orgs_list1.txt: Firmicutes
cons_orgs_list2.txt: Proteobacteria

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 22 14:34:44 2005 UTC (14 years, 9 months ago) by fangfang
Branch: MAIN
Changes since 1.5: +2 -2 lines
Diff to previous 1.5
Fixed a bug in creating multirows for one gene search key.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 22 06:58:01 2005 UTC (14 years, 9 months ago) by fangfang
Branch: MAIN
Changes since 1.4: +90 -83 lines
Diff to previous 1.4
Now support multiple hits for one gene search key.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 18 05:21:41 2005 UTC (14 years, 9 months ago) by fangfang
Branch: MAIN
Changes since 1.3: +12 -9 lines
Diff to previous 1.3
Changed the directory to save master tables on uchicago machines.

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 18 03:35:55 2005 UTC (14 years, 9 months ago) by fangfang
Branch: MAIN
Changes since 1.2: +474 -20 lines
Diff to previous 1.2
Drug Targets Portal:

  View Existing Tables
  Work on New Tables

Five more columns of CLiBE energy information are added to the table.

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 10 23:26:45 2005 UTC (14 years, 9 months ago) by fangfang
Branch: MAIN
Changes since 1.1: +1 -1 lines
Diff to previous 1.1
Fixed a bug in downloading Excel table.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 10 21:24:19 2005 UTC (14 years, 9 months ago) by fangfang
Branch: MAIN
Pipeline for generating a DrugTargets table based on user input gene search keys.

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