7866457712
allows to change easiestly parameters
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2023-04-29 07:06:07 +02:00
5a7b869170
Add a better management of and create translation exception when required for initiation codon
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2023-04-29 07:04:09 +02:00
d6a97da963
Update README.md
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2022-02-28 10:09:47 +01:00
689fa98bcb
Update README.md (repseek now into NIX)
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2022-02-28 09:59:14 +01:00
2409494186
Take into account genes overlaping the circular junction
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2022-02-17 20:21:54 +01:00
3b43762ced
some blast tricks
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2022-02-17 18:43:15 +01:00
d75cb117d3
new script for sumarizing features for easiest compairison
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2022-02-17 18:42:55 +01:00
0f6b447c5c
Change the gitignore
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2022-02-17 18:41:46 +01:00
9d93a68b3a
Change setup for the blast filtering before exonerate
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2022-02-17 18:41:27 +01:00
3b584dbebd
Change rRNA gene name to rra16s and so on...
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2022-02-17 18:40:34 +01:00
18453afeae
Add dependency to GNU parallel
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2022-02-17 18:39:51 +01:00
3c11767520
Gitignore
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2022-02-16 22:55:09 +01:00
cc95db33e1
Gitingor
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2022-02-16 22:50:39 +01:00
831669433e
Switch to a swissprot based reference database for CDS annotation
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2022-02-16 22:50:17 +01:00
90b3ee9b04
Do correct renaming of RPS12 genes if several
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2022-02-14 15:29:02 +01:00
616fd2bb44
A script for helping in clustering reference database for CDS annotation
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2022-02-14 15:10:47 +01:00
05551549bf
Allows for specifying a start point for the locus tag numbering
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2022-02-14 15:10:03 +01:00
d56aeaf698
Remove extra feature for CDS
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2022-02-14 15:09:17 +01:00
1d18a6f720
Merge branch 'master' of ssh://git.metabarcoding.org/org-asm/org-annotate
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2022-02-14 14:21:56 +01:00
59fcad1c42
Adds detection of RPS12 and managment of locus tags
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2022-02-14 14:21:50 +01:00
00454a529e
Update README.md to list every nix packages corresponding to org.annot dependences
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2021-11-08 10:33:06 +01:00
eb2bd2ce05
Update README.txt name to .md
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2021-11-08 10:21:06 +01:00
1eb97d34ff
Update README.txt to switch to Markdown format
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2021-11-08 10:20:23 +01:00
9648bbb874
Makes modification on the sequence header and feature source
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2021-11-05 09:30:55 +01:00
616d5d084b
change tRNA and CDS annotations
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2021-11-05 09:29:57 +01:00
27c02dfc1b
Patch the name of rRNA genes
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2021-11-04 21:59:46 +01:00
775d1a7157
Adds changes to conform with EMBL template files
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2021-11-04 21:55:59 +01:00
59a53bf482
Patch the detection algorithm (the overlap detection)
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2021-11-04 13:42:35 +01:00
12b4f27a01
Adds new options and call the new bash version of go_cds
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2021-11-04 13:38:45 +01:00
e4627ced6e
Switch the go_cds script from tcsh to bash
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2021-11-04 13:36:28 +01:00
fde0208b21
Small indentation change
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2021-11-03 13:20:21 +01:00
2c1d15c227
Adds the detection of the RPS12 gene (Gene with trans-splicing)
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2021-11-03 13:19:01 +01:00
8e6449bec6
Adds options to allows to disconnect some detectors
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2021-06-01 09:54:04 +02:00
40feaadd43
Move the script used for clusterizing protein DBs
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2021-06-01 09:53:10 +02:00
ac83c2db7c
add a -l option to set a minimum length on the contig to annotate
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2019-04-05 13:05:35 +02:00
15f033332c
Patch a bug leading to a double pseudogene tagging
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2018-11-20 17:39:38 +01:00
2ff6ff3308
If proteins are looked for without stop adds an extra option
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PASS1_LOOK_FOR_PSEUDO allowing for searching with stop in a second time
(Pseudogene search).
The PASS1_ALLOW_STOP is set back to 0 and the new PASS1_LOOK_FOR_PSEUDO
is set to 1
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2018-11-20 16:02:23 +01:00
a040adb132
Check the translation for stop codon and add a pseudogene qualifier if
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present.
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2018-11-20 15:59:57 +01:00
671c12605a
Merge branch 'master' of ssh://git@git.metabarcoding.org/org-asm/org-annotate.git
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2018-11-20 10:21:10 +01:00
47800462da
Add .DS_Store to the .gitignore files
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2018-05-11 16:52:21 +02:00
3ddeda464a
Add .DS_Store to the .gitignore files
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2018-05-11 16:50:25 +02:00
136c9ee7f6
Correct .gitignore files
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2018-05-11 16:35:28 +02:00
4f18ef51d0
Redirect output of pushd and popd to /dev/null
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2018-05-11 16:20:39 +02:00
812fdfa06f
Switch to version 2.4.0 of exonerate
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2018-05-11 16:19:30 +02:00
5a1c8283db
Freshly regerenrated CAU tRNA reference library with the new tool script
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2018-04-05 18:31:49 +02:00
405c89ea47
Add eclipse project files
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2018-04-05 18:16:07 +02:00
c691818059
Changes in .gitignore
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2018-04-05 18:15:40 +02:00
9070b54732
Switch to clustal-omega version 1.2.4
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2018-04-05 18:02:01 +02:00
9bcfa914fe
Switch to version 1.2.38 of aragorn
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2018-04-05 18:01:01 +02:00
0a5a65ab26
Change the notation algorithm to take advantage of the new CAU tRNA
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reference library
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2018-04-05 17:59:12 +02:00
