r2dt-bio · AntonPetrov · Nov 15, 2024 · Nov 15, 2024 · Nov 15, 2024 · Nov 15, 2024
diff --git a/data/tmrna/cm/all.cm b/data/tmrna/cm/all.cm
diff --git a/data/tmrna/cm/all.fa b/data/tmrna/cm/all.fa
@@ -0,0 +1,39 @@
+>tmRNA
+GGGGGUGAACUGGUUUCGACGGGAAUGUUGAUUCCAAAAGCUGCAUGCCGAGGUUGCCGG
+UGACCUCGUAAAACAACCGGCAAAAAAAUAAAUGCCAACAAUAAUUACUAUCGCUCUCGC
+UGCUUAAUAAGCAGCGAGCCGUCCCCCCAGCCCUUGCCUGUUGGGCUGGGAAGGGGCGUC
+AUAAAAGCGGGAUAGCCUUUAGGUUUGCCUGGGGCCUAAAGGCGAAAAUUAAAGAGGCUA
+GCCUUAAGGAAGCCUGUCUGUUGGCAUCCUUAAGGCGAAAAUAAAAAACAGACUAAGCAU
+GUAGAAGCUUUUGGAAUAACAUUUUCGGACGCGGGUUCGAUUCCCGCCACCUCCACCA
+>tmRNA_intron
+GGGGGUGAAUGGUUUCGACGGGGGGCCCUAGCGCCAAGGUUGCAUGCCGAGGAUGCCGGC
+GACCUCGUUAAAAAGCCGGCAAAAAUAUAAAUGCCAACAAUAAUAACUACGCUUUCGCUG
+CUUAAUGCAGCGAAGACGUCCUCCCCCUCCUCGCCUGAUGGAGGGGGAAAGGGCGUCAUU
+AAAGCGGGCUAGCCCACCCCAUUGCUUUGGGGGGGUGGGCGAAAAAUAAAAAGGCUGGCC
+UUAGCGCACCCUGUCUUUCGGGAGCGCUAAGGCGAAAAUAAAAAAGAGACUAAGCAUGUA
+GAAACCUUGGCGCUGGGCCCUCCGGACGCGGGUUCGAUUCAAAAAGAGUCGCCCUGGGGG
+GUAACCCCCAGGGGAAAACCCGGCUAAAUCAGGGAAACCCUAACCUGAAAGAAGGCUAGG
+GUAAUCCUGAGGGGUGCCCCGAAACGGGGAACCUGCAGAGACUCUGGCCCCCCUAAAAGG
+GGGGACCAGAUGGGAGGCAAAAUCGUUGAAUAAGUUUUAGAAUGCCUCCCAUAAAACGCC
+GGGCAUCCCGAAAGGGAUGAAGAGAUAGUCCACGCCCCUUGGAAAAUGGGGUAUACGUGU
+CCCGCCACCUCCACCA
+>tmRNA_alpha
+GCCCUUUAAAUUUUAAACAUAUUCUCCUAUAUUAGUAGUGCCGGUUUGCCGGCUAUGGCG
+AUAAACGCCCCGCGUAAUAAACGCAUCGGACCCGGGGGCGGUACCCGGCGCCUCCACCAA
+AAACCUUUCAUUUAUGUGUUUUUUUAUGGGGGCGAAAUAGGAUCGACGAGCGUGUAAAGG
+CGGGGCUUUCGCCCGGUAUGGUGCCACCGUUAUCGGCCCAAAAUUAUAAUUGCAAACGAC
+AACUAUGCUCCGGUUGCUCUUGCUGCGUAAGCAGUUUGAAAAAUUGAAAUUUAAGUCCUA
+AGGGUUAGCACCGUUAGGCGGGGUUCGGGGGCACCUGGCAACAGAAGCCCCCACU
+>tmRNA_beta
+ACACGCAAAUUGACUUGAAGCUGACGGCAACGCGCGUAUAAUCUAGAGCAUGGUUGUAUU
+CCGGCAACCUGGAGGCGUUCUGGACGGGGGUUCGAUUCCCCCCACCUCCACCCAAGGGCA
+UUCCACGGAGAGUGUUUAGAUGGGGGUGUACUGGUUUCGACAGGGCGGGCAAAGGUGAGC
+AGGCAACCCGUCAGGCGACGGACGUUAAUAAUGCAAAUCCAUAAAUGCCAACGAUGAGCA
+UUUCGCAAUGGCCGCCUAAAAACGGCUAGCCGGGGCUGCUGCUGCCUUGUUACCAAAGAG
+CAGCCGGCGGGGGCCUCGGGGCCCCCGCUCA
+>tmRNA_cyano
+CUGUCAGAAUAAAAAUGUCCGGCUUUAGCCGGACUAGGUGACCCACACCACUGUCCCGGA
+CAGCGGUUCGAUUCCGCUCAGCUCCAUUCCUCCUUCUUGGGGCUGCAAUGGUUUCGACGG
+GGCAGAAGGAGGGUGACUGAAGCCUGCUCGGUUAGAGCAAAAACAUAACUGCUAACAACA
+UCGUUAGUUUCUCCCGCCCAGCAGCCCCUGUGGCUGCCUGAGCCUUUAAAGGAGAUGGGG
+CGAGGUCAGCCUUAUCACCCAAAUGACCCAUGGGGCCCGGAAGGGCCC
diff --git a/data/tmrna/cm/all.fa.ndb b/data/tmrna/cm/all.fa.ndb
diff --git a/data/tmrna/cm/all.fa.nhr b/data/tmrna/cm/all.fa.nhr
diff --git a/data/tmrna/cm/all.fa.nin b/data/tmrna/cm/all.fa.nin
diff --git a/data/tmrna/cm/all.fa.njs b/data/tmrna/cm/all.fa.njs
@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "all.fa",
+  "dbtype": "Nucleotide",
+  "db-version": 5,
+  "description": "all.fa",
+  "number-of-letters": 1948,
+  "number-of-sequences": 5,
+  "last-updated": "2025-01-17T12:30:00",
+  "number-of-volumes": 1,
+  "bytes-total": 37963,
+  "bytes-to-cache": 643,
+  "files": [
+    "all.fa.ndb",
+    "all.fa.nhr",
+    "all.fa.nin",
+    "all.fa.not",
+    "all.fa.nsq",
+    "all.fa.ntf",
+    "all.fa.nto"
+  ]
+}
diff --git a/data/tmrna/cm/all.fa.not b/data/tmrna/cm/all.fa.not
diff --git a/data/tmrna/cm/all.fa.nsq b/data/tmrna/cm/all.fa.nsq
diff --git a/data/tmrna/cm/all.fa.ntf b/data/tmrna/cm/all.fa.ntf
diff --git a/data/tmrna/cm/all.fa.nto b/data/tmrna/cm/all.fa.nto
diff --git a/data/tmrna/cm/modelinfo.txt b/data/tmrna/cm/modelinfo.txt
@@ -0,0 +1,6 @@
+*all* - - all.cm
+tmRNA tmRNA Bacteria tmRNA.cm
+tmRNA_intron tmRNA Bacteria tmRNA_intron.cm
+tmRNA_alpha tmRNA Alphaproteobacteria tmRNA_alpha.cm
+tmRNA_beta tmRNA Betaproteobacteria tmRNA_beta.cm
+tmRNA_cyano tmRNA Cyanobacteria tmRNA_cyano.cm
diff --git a/data/tmrna/cm/tmRNA.cm b/data/tmrna/cm/tmRNA.cm
diff --git a/data/tmrna/cm/tmRNA_alpha.cm b/data/tmrna/cm/tmRNA_alpha.cm
diff --git a/data/tmrna/cm/tmRNA_beta.cm b/data/tmrna/cm/tmRNA_beta.cm
diff --git a/data/tmrna/cm/tmRNA_cyano.cm b/data/tmrna/cm/tmRNA_cyano.cm
diff --git a/data/tmrna/cm/tmRNA_intron.cm b/data/tmrna/cm/tmRNA_intron.cm
diff --git a/data/tmrna/fasta/tmRNA.fasta b/data/tmrna/fasta/tmRNA.fasta
@@ -0,0 +1,3 @@
+>tmRNA
+GGGGGUGAACUGGUUUCGACGGGAAUGUUGAUUCCAAAAGCUGCAUGCCGAGGUUGCCGGUGACCUCGUAAAACAACCGGCAAAAAAAUAAAUGCCAACAAUAAUUACUAUCGCUCUCGCUGCUUAAUAAGCAGCGAGCCGUCCCCCCAGCCCUUGCCUGUUGGGCUGGGAAGGGGCGUCAUAAAAGCGGGAUAGCCUUUAGGUUUGCCUGGGGCCUAAAGGCGAAAAUUAAAGAGGCUAGCCUUAAGGAAGCCUGUCUGUUGGCAUCCUUAAGGCGAAAAUAAAAAACAGACUAAGCAUGUAGAAGCUUUUGGAAUAACAUUUUCGGACGCGGGUUCGAUUCCCGCCACCUCCACCA
+(((((((............((((((((((.((((((((((((.(((((......(((((((..............)))))))..................................(((((((.......)))))))..((((((((((((((.........))))))))..))))))................(((((((((...........))))))))).................((((((((((.(((........))).))))))))))....................)))))....))))))))))))))))))))))...(((((.......))))))))))))....
diff --git a/data/tmrna/fasta/tmRNA_alpha.fasta b/data/tmrna/fasta/tmRNA_alpha.fasta
@@ -0,0 +1,3 @@
+>tmRNA_alpha
+GCCCUUUAAAUUUUAAACAUAUUCUCCUAUAUUAGUAGUGCCGGUUUGCCGGCUAUGGCGAUAAACGCCCCGCGUAAUAAACGCAUCGGACCCGGGGGCGGUACCCGGCGCCUCCACCAAAAACCUUUCAUUUAUGUGUUUUUUUAUGGGGGCGAAAUAGGAUCGACGAGCGUGUAAAGGCGGGGCUUUCGCCCGGUAUGGUGCCACCGUUAUCGGCCCAAAAUUAUAAUUGCAAACGACAACUAUGCUCCGGUUGCUCUUGCUGCGUAAGCAGUUUGAAAAAUUGAAAUUUAAGUCCUAAGGGUUAGCACCGUUAGGCGGGGUUCGGGGGCACCUGGCAACAGAAGCCCCCACU
+.......................................(((((....)))))...(((((.....(((((((........(((.(((...(((((.......)))))(((((((................................)))))))............)))))).......)))))))..))))).....(((.(((.........))))))..........................................................................................................((((((..............))))))...
diff --git a/data/tmrna/fasta/tmRNA_beta.fasta b/data/tmrna/fasta/tmRNA_beta.fasta
@@ -0,0 +1,3 @@
+>tmRNA_beta
+ACACGCAAAUUGACUUGAAGCUGACGGCAGCGCGCGUAUAAUCUAGAGCAUGGUUGUAUUCCGGCAACCUGGAGGCGUUCUGGACGGGGGUUCGAUUCCCCCCACCUCCACCCAAGGGCAUUCCACGGAGAGUGUUUUGAUGGGGGUGUACUGGUUUCGACAGGGCGGGCAAAGGUGAGCAGGCAACCCGUCAGGCGACGGACGUUAAUAAUACAAAUCCAUAAAUGCCAACGAUGAGCAUUUCGCAAUGGCCGCCUAAAAACGGCUAGCUGGGGCUGCUGCUGCCUUGUUACCAAAGAGCAGCCGCCGGGGGCCUCGGGGCCCCCGGUCA
+...................................................(((((....((.((.((((.....(((((((...(((((.......)))))(((((((................................)))))))............))))))).....))))..)).)))))))((((........)))).........................................................................((((((...............))))))..(((((((((....)))))))))...
diff --git a/data/tmrna/fasta/tmRNA_cyano.fasta b/data/tmrna/fasta/tmRNA_cyano.fasta
@@ -0,0 +1,3 @@
+>tmRNA_cyano
+CUGUCAGAAUAAAAAUGUCCGGCUUUAGCCGGACUAGGUGACCCACACCACUGUCCCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCCUCCUUCUUGGGGCUGCAAUGGUUUCGACGGGGCAGAAGGAGGGUGACUGAAGCCUGCUCGGUUAGAGCAAAAACGUAACUGCUAACAACAUCGUUAGUUUCUCCCGCCCAGCCGCCCCUGUGGCGGCCUGAGCCUUUAAAGGAGAUGGGGCGAGGUCAGCCUUAUCACCCAAAUGACCCAUGGGGCCCGGAAGGGCCC
+................(((((((....)))))))..(((.((((...((.((((((((...(((((.......)))))(((((((.............)))))))............))))))))..)).)))).)))......(((((.....))))).....................................(.(((.((((.....))))..))).)........((.((((((((.......))))))))..))............((((((....))))))
diff --git a/data/tmrna/fasta/tmRNA_intron.fasta b/data/tmrna/fasta/tmRNA_intron.fasta
@@ -0,0 +1,3 @@
+>tmRNA_intron
+GGGGGUGAAUGGUUUCGACGGGGGGCCCUAGCGCCAAGGUUGCAUGCCGAGGAUGCCGGCGACCUCGUUAAAAAGCCGGCAAAAAUAUAAAUGCCAACAAUAAUAACUACGCUUUCGCUGCUUAAUGCAGCGAAGACGUCCUCCCCCUCCUCGCCUGAUGGAGGGGGAAAGGGCGUCAUUAAAGCGGGCUAGCCCACCCCAUUGCUUUGGGGGGGUGGGCGAAAAAUAAAAAGGCUGGCCUUAGCGCACCCUGUCUUUCGGGAGCGCUAAGGCGAAAAUAAAAAAGAGACUAAGCAUGUAGAAACCUUGGCGCUGGGCCCUCCGGACGCGGGUUCGAUUCAAAAAGAGUCGCCCUGGGGGGUAACCCCCAGGGGAAAACCCGGCUAAAUCAGGGAAACCCUAACCUGAAAGAAGGCUAGGGUAAUCCUGAGGGGUGCCCCGAAACGGGGAACCUGCAGAGACUCUGGCCCCCCUAAAAGGGGGGACCAGAUGGGAGGCAAAAUCGUUGAAUAAGUUUUAGAAUGCCUCCCAUAAUACGCCGGGCAUCCCGAAAGGGAUGAAGAGAUAGUCCACGCCCCUUGGAAAAUGGGGUAUACGUGUCCCGCCACCUCCACCA
+(((((((...........((((((((((.((((((((((((.(((((......(((((((..............))))))).................................(((((((.....)))))))...((((((((((((((.........))))))))..))))))................(((((((((...........))))))))).................((((((((((.(((........))).))))))))))....................)))))....))))))))))))))))))))))...(((((..((((((.....)))))).((((((((....))))))))......((((((....((((((...(((((..............)))))...))))))(((...(((((...)))))..)))..........(((((((((.....)))))).))).(((((((((.........................))))))))).....))))))((((((....))))))...............((((.........)))).........))))))))))))....