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Freshly regerenrated CAU tRNA reference library with the new tool script

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Former-commit-id: b2808b9d4462c32d0d81fd4f8d134fb94ad9b51c
Former-commit-id: a1db9d37bba3adf1100c4418b9211aa49aa00da7
This commit is contained in:
Eric Coissac
2018-04-05 18:31:49 +02:00
parent 405c89ea47
commit 5a1c8283db
2 changed files with 21 additions and 62 deletions
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62
data/trna/CAU_tRNA_DB.fasta
View File

@ -6,12 +6,6 @@ acctacttaactcagtggttagagtactgctttcatacggcgggagtcattggttcaaatccaatagtaggta
gcatccatggctgaatggttaaagcgcccaactcataattggcgaattcgtaggttcaattcctactggatgcac
>trnI_AC_000188 gbac=AC_000188; trna=trnI; taxid=4081; distance=1;
gcatccatggctgaatggttaaagcgcccaactcataattggcgaattcgtaggttcaattcctactggatgcac
>trnM_NC_000925 gbac=NC_000925; trna=trnM; taxid=2787; distance=1;
tgcatctgtggccgaggggccgaaggcagcggactcataatccgccatttcgaaagagacgtcgctggttcgaatccagccagatgcat
>trnfM_NC_000925 gbac=NC_000925; trna=trnfM; taxid=2787; distance=2;
tcgcggggtagagcagtctggtagctcgtcgggctcataacccgaaggtcaatggttcaaatccattccccgctat
>trnI_NC_000925 gbac=NC_000925; trna=trnI; taxid=2787; distance=1;
tggctcagtagctcagtggttagagcaggggattcataagcccaaggtcgcaggttcaaatcccgcttgagccat
>trnM_NC_000927 gbac=NC_000927; trna=trnM; taxid=31312; distance=1;
gcctgcttagctcagttggttagagcgtccgtttcatacgcggattgtcactagttcaaatctagtagcaggcac
>trnfM_NC_000927 gbac=NC_000927; trna=trnfM; taxid=31312; distance=0;
@ -36,12 +30,6 @@ tgcctacttaactcagtggttagagtattgctttcatacggcgggagtcattggttcaaatccaatagtaggtag
gcatccatggctgaatggttaaagcgcccaactcataattggtaaatttgcgggttcaattcctgctggatgcac
>trnI_NC_001666 gbac=NC_001666; trna=trnI; taxid=4577; distance=1;
gcatccatggctgaatggttaaagcgcccaactcataattggtaaatttgcgggttcaattcctgctggatgcac
>trnfM_NC_001675 gbac=NC_001675; trna=trnfM; taxid=2762; distance=0;
cgcggagtagagcagtttggtagctcgtcgggctcataacccgaaggtcagtggttcaaatccactctccgcaa
>trnM_NC_001675 gbac=NC_001675; trna=trnM; taxid=2762; distance=2;
tgcatctgtggccgagcggttgaaggcagcgggctcataatccgtcatctgaaaagatatcactggttcgaatccagtcagatgcatc
>trnI_NC_001675 gbac=NC_001675; trna=trnI; taxid=2762; distance=1;
tggctcggtagctcagtggtagagcaggggactcataagcccttggtcgtgggttcaaatcccacttgagccat
>trnI_NC_001865 gbac=NC_001865; trna=trnI; taxid=3077; distance=0;
gcacctatggcagagtggtcgattgcaccgcactcataatgcggtttcgaaagaacatcgttggttcaaacccaactgggtgca
>trnfM_NC_001865 gbac=NC_001865; trna=trnfM; taxid=3077; distance=0;
@ -70,12 +58,6 @@ acctacttaactcagcggttagagtattgctttcatacggcgggagtcattggttcaaatccaatagtaggta
gcatccatggctgaatggttaaagcgcccaactcataattggcgaattcgtaggttcaattcctactggatgcac
>trnI_NC_002202 gbac=NC_002202; trna=trnI; taxid=3562; distance=1;
gcatccatggctgaatggttaaagcgcccaactcataattggcgaattcgtaggttcaattcctactggatgcac
>trnI_NC_002652 gbac=NC_002652; trna=trnI; taxid=3037; distance=1;
tgcatttatggcagagaggacgatagcacgggactcataatctcgttccgaaaggacatcgctggttcaaatccagctgaatgcat
>trnfM_NC_002652 gbac=NC_002652; trna=trnfM; taxid=3037; distance=0;
ggcgaagtagagtaaaaggttagctcgtgggcctcatgaccccaaggttaaaggttcgaatcctttcttcgcca
>trnM_NC_002652 gbac=NC_002652; trna=trnM; taxid=3037; distance=0;
ggttcaatagctcaaaggtagagcataggattcataagcctcaggtcacaagttcaaatcttgtttgaacca
>trnfM_NC_002762 gbac=NC_002762; trna=trnfM; taxid=4565; distance=2;
gagcggagtagagcagtttggtagctcacgaggctcataaccttgaggtcacgggttcgattcccgtctccgcact
>trnM_NC_002762 gbac=NC_002762; trna=trnM; taxid=4565; distance=1;
@ -116,12 +98,6 @@ cgcggggtggagcagcttggtagctcgcgaggctcataacctcgaggtcacgggttcaaatcccgtctccgcaa
gcctacttaactcagcggtgagagtatcgctttcatacggcgagagtcattggttcgaatccaatagtaggta
>trnI_NC_004766 gbac=NC_004766; trna=trnI; taxid=13818; distance=0;
gcatccatggctgaacggtcaaagcacccaactcataattggcgaattcacaggttcaactcctgttggatgca
>trnM_NC_004799 gbac=NC_004799; trna=trnM; taxid=280699; distance=1;
tgcatctatggccgagcggcttaaggcagcggactcataatccgtggacaagaatttgtcatcgctggttcgaatccagctggatgcat
>trnfM_NC_004799 gbac=NC_004799; trna=trnfM; taxid=280699; distance=0;
cgcggagtagagcagtctggtagctcgtcgggctcataacccgaaggccaatggttcaaatccattctccgcta
>trnI_NC_004799 gbac=NC_004799; trna=trnI; taxid=280699; distance=0;
ggctcagtagctcagaggttagagcgggggactcataagcctcaggtcgtaggttcaaatcttacctgagcca
>trnfM_NC_005086 gbac=NC_005086; trna=trnfM; taxid=13333; distance=0;
cgcggggtagagcagtttggtagctcgcaaggctcataaccttgaggtcacgggttcaaatcctgtctccgcaa
>trnM_NC_005086 gbac=NC_005086; trna=trnM; taxid=13333; distance=1;
@ -320,18 +296,6 @@ acctacttaactcagtggttagagtattgctttcatacggcgagagtcattggttcaaatccaatagtaggta
gcatccatggctgaatggttaaagcgcccaactcataattggcgaattcgtaggttcaattcctactggatgcac
>trnI_NC_008535 gbac=NC_008535; trna=trnI; taxid=13443; distance=1;
gcatccatggctgaatggttaaagcgcccaactcataattggcgaattcgtaggttcaattcctactggatgcac
>trnI_NC_008588 gbac=NC_008588; trna=trnI; taxid=2850; distance=0;
ggctctgtagctcagtggttagagcaggggactcataagcccaaggtcgtaggttcaaatcccaccagagcca
>trnfM_NC_008588 gbac=NC_008588; trna=trnfM; taxid=2850; distance=1;
tcgcggagtagagcagcctggtagctcgttgggctcataacccgaaggtcaatggttcaaatccattctccgctag
>trnM_NC_008588 gbac=NC_008588; trna=trnM; taxid=2850; distance=1;
tgcattcgtggccgagtggttgaaggcaccggactcataatccgttttcctctggaacgtcactggttcgaacccagtcgaatgcag
>trnM_NC_008589 gbac=NC_008589; trna=trnM; taxid=35128; distance=0;
gcattcgtggccgagtggttgaaggcaccggactcataatccgttttcctctggaacgtcactggttcgaacccagtcggatgca
>trnI_NC_008589 gbac=NC_008589; trna=trnI; taxid=35128; distance=0;
ggctctgtagctcagtggttagagcaggggactcataagcccaaggtcgtaggttcaaatcccaccagagcca
>trnfM_NC_008589 gbac=NC_008589; trna=trnfM; taxid=35128; distance=1;
tcgcggagtagagcagtctggtagctcgttgggctcataacccgaaggtcaatggttcaaatccattctccgctag
>trnfM_NC_008590 gbac=NC_008590; trna=trnfM; taxid=112509; distance=1;
gagcggagtagagcagtttggtagctcacgaggctcataaccttgaggtcacgggttcgattcccgtctccgcact
>trnM_NC_008590 gbac=NC_008590; trna=trnM; taxid=112509; distance=1;
@ -732,12 +696,6 @@ acctacttaactcagtggttagagtattgctttcatacggcaggagtcattggttcaaatccaatagtaggta
cgcggagtagagcaacttggtagctcgcaaggctcataaccttgaggtcacgggttcaaatcccgtctccgcaac
>trnI_NC_011163 gbac=NC_011163; trna=trnI; taxid=3827; distance=1;
gcatccatggctgaatggttaaagcacccaactcataattggcgaagtcgtaggttcaattcctactggatgcac
>trnI_NC_011600 gbac=NC_011600; trna=trnI; taxid=109269; distance=1;
tggctttgtagctcagtggttagagcaggggactcataagcccaaggtcgcaggttcaaatcccgccaaagccaa
>trnM_NC_011600 gbac=NC_011600; trna=trnM; taxid=109269; distance=1;
tgcatccgtggccgagcggttgatggcaacgggctcataatccgttttcctttggaacaccactggttcaaatccagtcggatgcaa
>trnfM_NC_011600 gbac=NC_011600; trna=trnfM; taxid=109269; distance=0;
agcggagtagagcagcatggtagctcgttgggctcataacccgaaggtcagaggttcaaatccactctccgcta
>trnI_NC_011828 gbac=NC_011828; trna=trnI; taxid=3900; distance=1;
gcatccatggctgaatggttaaagcacccaactcataattggcgaagtcgtaggttcaattcctactggatgcac
>trnfM_NC_011828 gbac=NC_011828; trna=trnfM; taxid=3900; distance=1;
@ -828,20 +786,6 @@ acctacttaactcagtggttagagtattgctttcatacggcaggagtcattggttcaaatccaatagtaggta
ggcggagtggagcaacttggtagctcgcaaggctcataaccttgaggttacgggttcaaatcctgtctccgcacc
>trnI_NC_014063 gbac=NC_014063; trna=trnI; taxid=3860; distance=0;
gcatccatggctgagtggttaaagcacccaactcataattggcgaagtcgtgggttcaattcctactggatgca
>trnfM_NC_014340 gbac=NC_014340; trna=trnfM; taxid=505693; distance=0;
aatgaaatagagcagtatggccagctcgccgggctcatgccccggaggtcacaggttcaactcctgttttcatta
>trnI_NC_014340 gbac=NC_014340; trna=trnI; taxid=505693; distance=0;
gactctgtagcttagttggttagagcatgggattcataagcccaaggtcgtaggttcaaatccaaccagagtca
>trnM_NC_014340 gbac=NC_014340; trna=trnM; taxid=505693; distance=0;
atacctatggctgagaggtcgaaagcactagactcataatctagctccaaatggaatcgatggttcaaatccatctaggtata
>trnI_NC_014345 gbac=NC_014345; trna=trnI; taxid=348535; distance=0;
ggctctgtagctcagtaggtcagagcgcgggactcataagcccaaggccgcaggttcaaatcctgccagagtcac
>trnM_NC_014345 gbac=NC_014345; trna=trnM; taxid=348535; distance=0;
gtacccgtggctgagcggtcgaaagcgatggactcataatccattctcttataagcatcagtggttcgaacccactcgggtaca
>trnfM_NC_014345 gbac=NC_014345; trna=trnfM; taxid=348535; distance=0;
ggcggggtagagcagcgcggtacagctcatcgggctcatgacccggaggtcagtggttcgaccccactccccgctc
>trnfM_NC_014345 gbac=NC_014345; trna=trnfM; taxid=348535; distance=0;
ggcggggtagagcagcgcggtacagctcatcgggctcatgacccggaggtcagtggttcgaccccactccccgctc
>trnfM_NC_014348 gbac=NC_014348; trna=trnfM; taxid=104588; distance=0;
cgcggggtagagcagcttggtagctcgcaaggctcataaccttgaggtcacgggttcaaatcctgtctccgcaa
>trnM_NC_014348 gbac=NC_014348; trna=trnM; taxid=104588; distance=0;
@ -2190,12 +2134,6 @@ gcctacttaactcagtggttagagtattgctttcatacggcagtagtcattggttcaaatccaatagtaggta
cgcggagtagagtagtttggtatctcgcaaggctcataaccttgagatcgcaggttcaaatcctgtctccgcaa
>trnI_NC_023132 gbac=NC_023132; trna=trnI; taxid=223125; distance=1;
gcatccatggctgaatggttaaagcgcccaactcataattggcgattttgtaggttcaattcctactggatgcac
>trnM_NC_023133 gbac=NC_023133; trna=trnM; taxid=35688; distance=0;
ggctcagtagctcagtggttagagcaggggactcataagcccaaggtcgcaggttcaaatcccgcctgagcca
>trnI_NC_023133 gbac=NC_023133; trna=trnI; taxid=35688; distance=0;
gcatctgtggccgagtggccgaaggcaacggactcataatccgtttctcgtaagagacgtcgctggttcgaacccagccggatgca
>trnfM_NC_023133 gbac=NC_023133; trna=trnfM; taxid=35688; distance=0;
cgcggggtagagcagtctggtagctcgtcgggctcataacccgaaagtcaatggttcaaatccattccccgcta
>trnfM_NC_023213 gbac=NC_023213; trna=trnfM; taxid=47600; distance=1;
cgcgggatagagcagtttggtagctcgcaaggctcataaccttgaggtcatgggttcaaatcccgttcccgcaac
>trnM_NC_023213 gbac=NC_023213; trna=trnM; taxid=47600; distance=0;

21
data/trna/CAU_tRNA_DB.log
View File

@ -16,3 +16,24 @@
2015-10-10 19:03:11 [OA INFO ] 63859 -- Done
2015-10-10 19:03:11 [OA INFO ] 63859 -- Installing the CAU tRNA database...
2015-10-10 19:03:11 [OA INFO ] 63859 -- Done
2018-04-05 18:17:45 [OA INFO ] 1072 -- Selecting Viridiplantae genebank entries...
2018-04-05 18:17:45 [OA INFO ] 1072 -- --> 0 entries selected
2018-04-05 18:17:45 [OA INFO ] 1072 -- Done
2018-04-05 18:17:45 [OA INFO ] 1072 -- Extracting the CAU tRNA from the plants entries...
2018-04-05 18:17:45 [OA INFO ] 1072 -- Done
2018-04-05 18:17:45 [OA INFO ] 1072 -- Installing the CAU tRNA database...
2018-04-05 18:17:45 [OA INFO ] 1072 -- Done
2018-04-05 18:18:34 [OA INFO ] 1170 -- Selecting Viridiplantae genebank entries...
2018-04-05 18:18:36 [OA INFO ] 1170 -- --> 0 entries selected
2018-04-05 18:18:36 [OA INFO ] 1170 -- Done
2018-04-05 18:18:36 [OA INFO ] 1170 -- Extracting the CAU tRNA from the plants entries...
2018-04-05 18:18:36 [OA INFO ] 1170 -- Done
2018-04-05 18:18:36 [OA INFO ] 1170 -- Installing the CAU tRNA database...
2018-04-05 18:18:36 [OA INFO ] 1170 -- Done
2018-04-05 18:19:01 [OA INFO ] 1778 -- Selecting Viridiplantae genebank entries...
2018-04-05 18:19:09 [OA INFO ] 1778 -- --> 461 entries selected
2018-04-05 18:19:09 [OA INFO ] 1778 -- Done
2018-04-05 18:19:09 [OA INFO ] 1778 -- Extracting the CAU tRNA from the plants entries...
2018-04-05 18:26:03 [OA INFO ] 1778 -- Done
2018-04-05 18:26:03 [OA INFO ] 1778 -- Installing the CAU tRNA database...
2018-04-05 18:26:03 [OA INFO ] 1778 -- Done