[Bio] Log of /FigKernelPackages/FS

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 30 02:22:52 2010 UTC (9 years, 3 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0928, rast_rel_2010_1206
Changes since 1.30: +2 -1 lines
Diff to previous 1.30

re-redirect nap stdout to /dev/null. here's hoping it works on windows still

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 27 19:23:32 2010 UTC (9 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.29: +2 -2 lines
Diff to previous 1.29

Change threshold

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 23 18:33:11 2010 UTC (9 years, 3 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0827
Changes since 1.28: +108 -24 lines
Diff to previous 1.28

More FS_RAST modes & supporting code for SAS use.

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 21 15:49:45 2010 UTC (9 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.27: +0 -55 lines
Diff to previous 1.27

removing dependencies

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 21 15:43:06 2010 UTC (9 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.26: +17 -16 lines
Diff to previous 1.26

removing dependencies

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 21 15:35:09 2010 UTC (9 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.25: +14 -3 lines
Diff to previous 1.25

fixed dependence on FIG.pm but not FIG_Config.pm

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 21 00:30:33 2010 UTC (9 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.24: +1 -1 lines
Diff to previous 1.24

nasty bug in frameshift correction

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 3 00:20:32 2009 UTC (10 years, 8 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526
Changes since 1.23: +136 -32 lines
Diff to previous 1.23

force frameshifts to be of longer chunks

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 24 17:01:53 2009 UTC (10 years, 8 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.22: +1 -1 lines
Diff to previous 1.22

fix to get rid of undefined value

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 5 14:33:02 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.21: +37 -33 lines
Diff to previous 1.21

fix contraints on gluing pieces

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 4 01:46:36 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_02_05
Changes since 1.20: +27 -5 lines
Diff to previous 1.20

fixes to seeing if two pieces can be glued together

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 1 21:05:11 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.19: +6 -6 lines
Diff to previous 1.19

it will catch more now

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 19 23:52:51 2008 UTC (11 years, 1 month ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_rel_2008_11_24, rast_rel_2008_12_18
Changes since 1.18: +43 -6 lines
Diff to previous 1.18

fixes to detecting consistent fragments

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jul 5 15:53:08 2008 UTC (11 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806, rast_rel_2008_07_21, rast_rel_2008_08_07
Changes since 1.16: +68 -9 lines
Diff to previous 1.16

fixes to grouping

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 15 13:43:00 2008 UTC (11 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2008_06_16, rast_rel_2008_06_18
Changes since 1.15: +67 -8 lines
Diff to previous 1.15

fix to computing locations for frameshifts

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 12 21:42:00 2008 UTC (11 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +6 -6 lines
Diff to previous 1.14

enlarge the fragment of DNA in which a hit is sought

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 3 12:27:41 2008 UTC (11 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.13: +12 -5 lines
Diff to previous 1.13

minor fixes relating to translation code

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 3 12:22:24 2008 UTC (11 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +43 -2 lines
Diff to previous 1.12

fix clean_span - it assumed positive strand

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 13 15:21:41 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.11: +3 -3 lines
Diff to previous 1.11

clean up name conflicts

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 9 14:05:06 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.10: +15 -2 lines
Diff to previous 1.10

fixes for nonstandard genetic code

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 9 02:02:51 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +9 -2 lines
Diff to previous 1.9

fixes to FS_RAST.pm to handle nonstandard genetic codes

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 5 15:35:52 2008 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +2 -2 lines
Diff to previous 1.8

additions to FIGfam maintenance

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 18 14:12:56 2007 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +3 -3 lines
Diff to previous 1.7

require valid starts and stops for frameshift correction

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 16 03:55:43 2007 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +103 -70 lines
Diff to previous 1.6

fixes to frameshift correction

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 8 23:27:10 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.5: +1 -0 lines
Diff to previous 1.5

remove trailing stop codon from translation

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 8 21:20:41 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.4: +64 -20 lines
Diff to previous 1.4

fixes to FS_RAST.pm for frameshift detection

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 3 18:42:17 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.3: +1 -1 lines
Diff to previous 1.3

fix reference to nap in FS_RAST.pm

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 2 18:41:53 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.2: +7 -0 lines
Diff to previous 1.2

fixes to add an extra alignment

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 21 20:41:05 2007 UTC (12 years ago) by overbeek
Branch: MAIN
Changes since 1.1: +150 -54 lines
Diff to previous 1.1

add code to fix frameshifts in a genome

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 21 13:36:05 2007 UTC (12 years ago) by overbeek
Branch: MAIN

add FS_RAST.pm, a module to support RAST searches correcting frameshifts

This form allows you to request diffs between any two revisions of this file. For each of the two "sides" of the diff, select a symbolic revision name using the selection box, or choose 'Use Text Field' and enter a numeric revision.

Links to HEAD:	(view) (download) (as text) (annotate)
Links to rast_rel_2010_1206:	(view) (download) (as text) (annotate)
Sticky Tag:

	Diffs between and
	Type of Diff should be a

Log of /FigKernelPackages/FS_RAST.pm