[Bio] / FigKernelPackages / find_homologs.pm Repository:
ViewVC logotype

Log of /FigKernelPackages/find_homologs.pm

Parent Directory Parent Directory


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

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 21 21:47:33 2015 UTC (5 years ago) by golsen
Branch: MAIN
CVS Tags: HEAD
Changes since 1.10: +56 -15 lines
Diff to previous 1.10
Make blast+ the default in find_nucleotide_homologs, solving an issue
with occasional errors in blastall output.
Add a new wrapper (find_RNA_genes) based on svr_RNA_genes, that does
not include SEED and/or Sappling genome support.
Do not copy the DNA file supplied by the user.
Add command line support for fraction sequence coverage.
Improve documentation.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 27 22:29:35 2014 UTC (6 years, 2 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.9: +1 -0 lines
Diff to previous 1.9
Remove unused references to FIG_Config.
add sas directive to find_homologs.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 7 22:31:03 2013 UTC (6 years, 5 months ago) by golsen
Branch: MAIN
Changes since 1.8: +38 -6 lines
Diff to previous 1.8
Add feature type to created features.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 1 18:55:20 2013 UTC (6 years, 6 months ago) by golsen
Branch: MAIN
Changes since 1.7: +40 -14 lines
Diff to previous 1.7
Improvements that decrease the splicing of blast HSPs for trivial coverage
gain.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 7 19:28:32 2012 UTC (7 years, 3 months ago) by golsen
Branch: MAIN
Changes since 1.6: +3 -2 lines
Diff to previous 1.6
Minor change to documentation (comments).
Change blast call to use two threads.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 19 16:37:14 2012 UTC (8 years ago) by golsen
Branch: MAIN
CVS Tags: mgrast_version_3_2
Changes since 1.5: +9 -3 lines
Diff to previous 1.5
Minor modifications to code to improve behavior in rRNA finding (if I
remember correctly).

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 7 00:37:05 2012 UTC (8 years, 2 months ago) by golsen
Branch: MAIN
Changes since 1.4: +5 -4 lines
Diff to previous 1.4
A minor change than prevents an error when there are no contigs to search.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 2 22:03:14 2011 UTC (9 years, 3 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_dev_05262011, mgrast_dev_06072011, mgrast_dev_08022011, mgrast_dev_08112011, mgrast_dev_10262011, mgrast_dev_12152011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_4, mgrast_release_3_1_0, mgrast_release_3_1_1, mgrast_release_3_1_2, myrast_33, myrast_rel40, rast_rel_2011_0119, rast_rel_2011_0928
Changes since 1.3: +113 -150 lines
Diff to previous 1.3
use SeedAware
Many changes in details of code.

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 22 14:38:13 2009 UTC (11 years, 1 month ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_03_26, rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206
Changes since 1.2: +13 -5 lines
Diff to previous 1.2
update from Gary

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 18 00:37:35 2009 UTC (11 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.1: +107 -69 lines
Diff to previous 1.1
updates for Gary Olsen

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 5 14:50:43 2009 UTC (11 years, 1 month ago) by overbeek
Branch: MAIN
fixes to support search for rRNAs

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.

  Diffs between and
  Type of Diff should be a

Sort log by:

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3