| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/gff3reader_test_cases_genbank/ |
| H A D | rw-451_LSVZ_Augustus.gff3 | 13 …+ 0 Parent=scaffold12160.g1.t1;product=pyruvate dehydrogenase phosphatase regulatory mitochondrial;
14 …cds;Parent=scaffold12160.g1.t1;product=pyruvate dehydrogenase phosphatase regulatory mitochondrial;
15 …cds;Parent=scaffold12160.g1.t1;product=pyruvate dehydrogenase phosphatase regulatory mitochondrial;
16 …cds;Parent=scaffold12160.g1.t1;product=pyruvate dehydrogenase phosphatase regulatory mitochondrial;
17 …cds;Parent=scaffold12160.g1.t1;product=pyruvate dehydrogenase phosphatase regulatory mitochondrial;
18 …cds;Parent=scaffold12160.g1.t1;product=pyruvate dehydrogenase phosphatase regulatory mitochondrial;
19 …+ 0 Parent=scaffold12160.g1.t1;product=pyruvate dehydrogenase phosphatase regulatory mitochondrial;
|
| /dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/TemplateModels/ |
| H A D | UniversalCode.def | 66 "Vertebrate mtDNA","Vertebrate mitochondrial DNA code. (Genebank transl_table=2).",
67 "Yeast mtDNA","Yeast mitochondrial DNA code. (Genebank transl_table=3).",
68 …"Mold/Protozoan mtDNA","Mold, Protozoan and Coelenterate mitochondrial DNA and the Mycloplasma/Spi…
69 "Invertebrate mtDNA","Invertebrate mitochondrial DNA code. (Genebank transl_table=5).",
71 "Echinoderm mtDNA","Echinoderm mitochondrial DNA code. (Genebank transl_table=9).",
74 "Ascidian mtDNA","Ascidian mitochondrial DNA code. (Genebank transl_table=13).",
75 "Flatworm mtDNA","Flatworm mitochondrial DNA code. (Genebank transl_table=14).",
|
| H A D | chooseGeneticCode.def | 48 "Vertebrate-mtDNA", "Vertebrate mitochondrial DNA code. (Genebank transl_table=2)."
50 "Yeast-mtDNA", "Yeast mitochondrial DNA code. (Genebank transl_table=3)."
52 …"Mold-Protozoan-mtDNA", "Mold, Protozoan and Coelenterate mitochondrial DNA and the Mycloplasma/Sp…
54 "Invertebrate-mtDNA", "Invertebrate mitochondrial DNA code. (Genebank transl_table=5)."
58 "Echinoderm-mtDNA", "Echinoderm mitochondrial DNA code. (Genebank transl_table=9)."
64 "Ascidian-mtDNA", "Ascidian mitochondrial DNA code. (Genebank transl_table=13)."
66 "Flatworm-mtDNA", "Flatworm mitochondrial DNA code. (Genebank transl_table=14)."
74 "Scenedesmus-obliquus-mtDNA", "Scenedesmus obliquus mitochondrial Code (transl_table=22)."
325 /* Scenedesmus obliquus mitochondrial Code */
|
| /dports/biology/emboss/EMBOSS-6.6.0/emboss/data/ |
| H A D | EGC.22 | 7 # found in mitochondrial DNA of Scenedesmus obliquus
30 # "The complete mitochondrial DNA sequence of Scenedesmus obliquus reflects an
31 # intermediate stage in the evolution of the green algal mitochondrial genome."
|
| H A D | EGC.index | 3 2 Vertebrate mitochondrial
4 3 Yeast mitochondrial
|
| H A D | EGC.23 | 6 # Added code 23 Thraustochytrium mitochondrial code
10 # This code has been created for the mitochondrial genome of the labyrinthulid
|
| /dports/biology/p5-BioPerl/BioPerl-1.7.7/t/data/ |
| H A D | testdbaccnums.out | 30 gnl|db1|NP_002444.1 (NM_002453) mitochondrial translational initiat... 21 204
42 gi|10|gnl|db1|NP_002444.1 (NM_002453) mitochondrial translational initiat... 21 204
174 >gnl|db1|NP_002444.1 (NM_002453) mitochondrial translational initiation factor 2
176 sp|P46199|IF2M_HUMAN Translation initiation factor IF-2, mitochondrial precursor
178 pir||A55628 translation initiation factor IF-2 precursor, mitochondrial - human
180 gb|AAM14617.1|AF494407_1 (AF494407) mitochondrial translation-initiation factor 2 [Homo
346 >gi|10|gnl|db1|NP_002444.1 (NM_002453) mitochondrial translational initiation factor 2
348 sp|P46199|IF2M_HUMAN Translation initiation factor IF-2, mitochondrial precursor
350 pir||A55628 translation initiation factor IF-2 precursor, mitochondrial - human
352 gb|AAM14617.1|AF494407_1 (AF494407) mitochondrial translation-initiation factor 2 [Homo
|
| H A D | U71225.gb | 4 gene, partial sequence, mitochondrial genes for mitochondrial RNAs.
|
| H A D | U71225.gb.mac | 4 gene, partial sequence, mitochondrial genes for mitochondrial RNAs.
|
| /dports/biology/py-biopython/biopython-1.79/Tests/Align/ |
| H A D | cow.fa | 35 >ref|XP_005212532.1| deoxyguanosine kinase, mitochondrial isoform X1 [Bos taurus]
70 >ref|NP_001091482.1| protoheme IX farnesyltransferase, mitochondrial [Bos taurus]
176 >ref|NP_001107989.1| cytochrome c oxidase subunit 8B, mitochondrial precursor [Bos taurus]
187 >ref|NP_787010.1| ATPase inhibitor, mitochondrial precursor [Bos taurus]
227 >ref|XP_024840318.1| presenilins-associated rhomboid-like protein, mitochondrial isoform X2 [Bos ta…
|
| /dports/biology/py-biopython/biopython-1.79/Tests/UniProt/ |
| H A D | gp_information.goa_yeast.28.gpi | 131 P00175 CYB2 Cytochrome b2, mitochondrial CYB2_YEAST|CYB2|YML054C|YM9958.08C protein taxon:559292 …
142 P00427 COX6 Cytochrome c oxidase subunit 6, mitochondrial COX6_YEAST|COX6|YHR051W protein taxon:559…
143 P00431 CCP1 Cytochrome c peroxidase, mitochondrial CCPR_YEAST|CCP1|CCP|CPO|YKR066C protein taxon:55…
145 P00447 SOD2 Superoxide dismutase [Mn], mitochondrial SODM_YEAST|SOD2|YHR008C protein taxon:559292 …
165 P00927 ILV1 Threonine dehydratase, mitochondrial THDH_YEAST|ILV1|YER086W protein taxon:559292 db_…
172 P01097 INH1 ATPase inhibitor, mitochondrial ATIF_YEAST|INH1|YDL181W|D1305 protein taxon:559292 db…
181 P02381 VAR1 Ribosomal protein VAR1, mitochondrial RMAR_YEAST|VAR1|Q0140 protein taxon:559292 db_s…
187 P02992 TUF1 Elongation factor Tu, mitochondrial EFTU_YEAST|TUF1|TUFM|YOR187W protein taxon:559292 …
200 P03881 Q0255 Uncharacterized mitochondrial protein RF1 YMRF1_YEAST|Q0255 protein taxon:559292 db_…
245 P05626 ATP4 ATP synthase subunit 4, mitochondrial ATPF_YEAST|ATP4|YPL078C|LPF7C protein taxon:55929…
[all …]
|
| H A D | gene_association.goa_yeast.1.gaf | 12 UniProtKB Q02486 ABF2 GO:0000001 PMID:9581629 IMP P ARS-binding factor 2, mitochondrial ABF2_YEAS…
13 UniProtKB P13433 RPO41 GO:0000002 PMID:3517858 IMP P DNA-directed RNA polymerase, mitochondrial R…
15 UniProtKB P22353 MRPL8 GO:0000002 PMID:2183197 IMP P 54S ribosomal protein L8, mitochondrial RM08…
16 …SH1 GO:0000002 PMID:1334021 IMP P DNA mismatch repair protein MSH1, mitochondrial MSH1_YEAST|MSH…
19 UniProtKB P32318 THI4 GO:0000002 PMID:9367751 IMP P Thiazole biosynthetic enzyme, mitochondrial T…
22 UniProtKB Q02486 ABF2 GO:0000002 PMID:9581629 IMP P ARS-binding factor 2, mitochondrial ABF2_YEAS…
44 UniProtKB P35191 MDJ1 GO:0000002 PMID:10567545 IMP P DnaJ homolog 1, mitochondrial MDJ1_YEAST|YFL…
45 UniProtKB P06168 ILV5 GO:0000002 PMID:7621838 IMP P Ketol-acid reductoisomerase, mitochondrial IL…
47 UniProtKB P19414 ACO1 GO:0000002 PMID:15692048 IMP P Aconitate hydratase, mitochondrial ACON_YEAS…
49 UniProtKB P54964 REX2 GO:0000002 PMID:9933355 IMP P Oligoribonuclease, mitochondrial ORN_YEAST|RE…
[all …]
|
| /dports/biology/emboss/EMBOSS-6.6.0/test/data/ |
| H A D | cutg.codon | 73 …658\1623\BAA78051.1\Dictyostelium discoideum\Dictyostelium discoideum mitochondrial DNA, complete …
75 …128\1467\BAA78052.1\Dictyostelium discoideum\Dictyostelium discoideum mitochondrial DNA, complete …
77 …994\1308\BAA78053.1\Dictyostelium discoideum\Dictyostelium discoideum mitochondrial DNA, complete …
79 …363\1344\BAA78054.1\Dictyostelium discoideum\Dictyostelium discoideum mitochondrial DNA, complete …
81 …62)\2295\BAA78055.1\Dictyostelium discoideum\Dictyostelium discoideum mitochondrial DNA, complete …
83 …8886\930\BAA78056.1\Dictyostelium discoideum\Dictyostelium discoideum mitochondrial DNA, complete …
85 …9678\789\BAA78057.1\Dictyostelium discoideum\Dictyostelium discoideum mitochondrial DNA, complete …
|
| /dports/biology/infernal/infernal-1.1.3/testsuite/ |
| H A D | 00README | 7 mito-celegans-trna.gb - Locations of 22 mitochondrial tRNAs [GDF]
8 mito-celegans-trna.fa - Sequences of 22 mitochondrial tRNAs. [FASTA]
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seqfeat/ |
| H A D | gc.prt | 13 -- Added Cephalodiscidae mitochondrial genetic code 33
41 -- Fixed capitalization of mitochondrial in codes 22 and 23
54 -- Added GTG start to Echinoderm mitochondrial code, code 9
57 -- Added code 23 Thraustochytrium mitochondrial code
63 -- found in mitochondrial DNA of Scenedesmus obliquus
80 -- based on complete mitochondrial genome of honeybee
|
| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seqfeat/ |
| H A D | gc.prt | 13 -- Added Cephalodiscidae mitochondrial genetic code 33
41 -- Fixed capitalization of mitochondrial in codes 22 and 23
54 -- Added GTG start to Echinoderm mitochondrial code, code 9
57 -- Added code 23 Thraustochytrium mitochondrial code
63 -- found in mitochondrial DNA of Scenedesmus obliquus
80 -- based on complete mitochondrial genome of honeybee
|
| /dports/biology/emboss/EMBOSS-6.6.0/emboss/data/TAXONOMY/ |
| H A D | gencode.dmp | 17 22 | | Scenedesmus obliquus mitochondrial | FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAA…
18 23 | | Thraustochytrium mitochondrial code | FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVA…
|
| /dports/biology/p5-BioPerl/BioPerl-1.7.7/t/data/map_hem/ |
| H A D | HEM1-HEM14.fa | 1 …ay; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expres…
51 >SGD_Scer_YER014W HEM14 "Protoporphyrinogen oxidase, a mitochondrial enzyme that catalyzes the seve…
|
| H A D | HEM13-HEM14.fa | 1 …zes the sixth step in the heme biosynthetic pathway; localizes to the mitochondrial inner membrane…
73 >SGD_Scer_YER014W HEM14 "Protoporphyrinogen oxidase, a mitochondrial enzyme that catalyzes the seve…
|
| H A D | HEM14-HEM15.fa | 1 >SGD_Scer_YER014W HEM14 "Protoporphyrinogen oxidase, a mitochondrial enzyme that catalyzes the seve…
29 >SGD_Scer_YOR176W HEM15 "Ferrochelatase, a mitochondrial inner membrane protein, catalyzes the inse…
|
| H A D | HEM1-HEM13.fa | 1 …ay; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expres…
51 …zes the sixth step in the heme biosynthetic pathway; localizes to the mitochondrial inner membrane…
|
| H A D | HEM1-HEM15.fa | 1 …ay; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expres…
51 >SGD_Scer_YOR176W HEM15 "Ferrochelatase, a mitochondrial inner membrane protein, catalyzes the inse…
|
| /dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/ |
| H A D | modellist.ibf | 83 (modelList [index])["Name"] = "mtMAM (mammalian mitochondrial)";
85 … S, Okada N, Paabo S, and Hasegawa M (1998) Conflict among individual mitochondrial proteins in re…
94 (modelList [index])["Name"] = "mtREV24 (vertebrate mitochondrial)";
96 …awa, M (1996) Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. E…
127 (modelList [index])["Name"] = "MtArt (arthropoda mitochondrial)";
128 …escription"] = "ML based. This model has been derived from 36 arthropoda mitochondrial genomes.";
|
| /dports/biology/ncbi-toolkit/ncbi/data/ |
| H A D | gc.prt | 28 -- Fixed capitalization of mitochondrial in codes 22 and 23
41 -- Added GTG start to Echinoderm mitochondrial code, code 9
44 -- Added code 23 Thraustochytrium mitochondrial code
50 -- found in mitochondrial DNA of Scenedesmus obliquus
67 -- based on complete mitochondrial genome of honeybee
|
| /dports/biology/jalview/jalview/resources/ |
| H A D | GeneticCodes.dat | 30 -- Fixed capitalization of mitochondrial in codes 22 and 23
43 -- Added GTG start to Echinoderm mitochondrial code, code 9
46 -- Added code 23 Thraustochytrium mitochondrial code
52 -- found in mitochondrial DNA of Scenedesmus obliquus
69 -- based on complete mitochondrial genome of honeybee
|