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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/unit_test/gff3writer_test_cases/
H A Dmss-346.bioseq.gff36 1000000 GenInfo mRNA 1 4001 . + . ID=rna-MSS-346;Parent=gene-MSS-346;gbkey=mRNA;gene=MSS-346
7 1000000 GenInfo exon 1 4001 . + . ID=exon-MSS-346-1;Parent=rna-MSS-346;gbkey=mRNA;gene=MSS-346
9 1000000 GenInfo mRNA 5001 9001 . + . ID=rna-MSS-346-2;Parent=gene-MSS-346;gbkey=mRNA;gene=MSS-346
10 1000000 GenInfo exon 5001 9001 . + . ID=exon-MSS-346-2-1;Parent=rna-MSS-346-2;gbkey=mRNA;gene=MSS-3…
13 1000000 GenInfo mRNA 10001 14001 . + . ID=rna-MSS-346-3;Parent=gene-MSS-346-2;gbkey=mRNA;gene=MSS-3…
14 1000000 GenInfo exon 10001 14001 . + . ID=exon-MSS-346-3-1;Parent=rna-MSS-346-3;gbkey=mRNA;gene=MSS…
22 1000000 GenInfo mRNA 20001 24001 . + . ID=rna-MSS-346-6;Parent=gene-MSS-346-3;gbkey=mRNA;gene=MSS-3…
23 1000000 GenInfo exon 20001 24001 . + . ID=exon-MSS-346-6-1;Parent=rna-MSS-346-6;gbkey=mRNA;gene=MSS…
25 1000000 GenInfo mRNA 25001 29001 . + . ID=rna-MSS-346-7;Parent=gene-MSS-346-3;gbkey=mRNA;gene=MSS-3…
31 1000000 GenInfo mRNA 30001 34001 . + . ID=rna-MSS-346-9;Parent=gene-MSS-346-4;gbkey=mRNA;gene=MSS-3…
[all …]
H A Dmss-360.annot.gff35 1000000 . mRNA 1 1001 . + . ID=rna-MSS-346;Parent=gene-MSS-346;gbkey=mRNA;gene=MSS-346
6 1000000 . exon 1 1001 . + . ID=exon-MSS-346-1;Parent=rna-MSS-346;gbkey=mRNA;gene=MSS-346
7 1000000 . CDS 1 1001 . + 0 ID=cds-MSS-346;Parent=rna-MSS-346;gbkey=CDS;gene=MSS-346
8 1000000 . mRNA 1001 2001 . + . ID=rna-MSS-346-2;Parent=gene-MSS-346;gbkey=mRNA;gene=MSS-346
10 1000000 . CDS 1001 2001 . + 0 ID=cds-MSS-346-2;Parent=rna-MSS-346-2;gbkey=CDS;gene=MSS-346
11 1000000 . mRNA 3001 4001 . . . ID=rna-MSS-346-3;Parent=gene-MSS-346;gbkey=mRNA;gene=MSS-346
13 1000000 . CDS 3001 4001 . . 0 ID=cds-MSS-346-3;Parent=rna-MSS-346-3;gbkey=CDS;gene=MSS-346
14 1000000 . mRNA 5001 6001 . + . ID=rna-MSS-346-4;Parent=gene-MSS-346;gbkey=mRNA;gene=MSS-346
16 1000000 . CDS 5001 6001 . + 0 ID=cds-MSS-346-4;Parent=rna-MSS-346-4;gbkey=CDS;gene=MSS-346
17 1000000 . mRNA 2001 3001 . - . ID=rna-1000000:2001..3001;gbkey=mRNA
[all …]
H A Dmodevidence-gnomon.annot.gff35 …rna-NW_004929286.1:1559..3530;Parent=gene-NW_004929286.1:1559..3530;Name=rna.229039288;gbkey=mRNA;…
6 …+ . ID=exon-NW_004929286.1:1559..3530-1;Parent=rna-NW_004929286.1:1559..3530;gbkey=mRNA;transcript…
7 …+ . ID=exon-NW_004929286.1:1559..3530-2;Parent=rna-NW_004929286.1:1559..3530;gbkey=mRNA;transcript…
8 …+ . ID=exon-NW_004929286.1:1559..3530-3;Parent=rna-NW_004929286.1:1559..3530;gbkey=mRNA;transcript…
9 …+ . ID=exon-NW_004929286.1:1559..3530-4;Parent=rna-NW_004929286.1:1559..3530;gbkey=mRNA;transcript…
10 …Parent=rna-NW_004929286.1:1559..3530;Name=GNOMON:229039288.p;gbkey=CDS;product=GNOMON:229039288.p;…
11 …Parent=rna-NW_004929286.1:1559..3530;Name=GNOMON:229039288.p;gbkey=CDS;product=GNOMON:229039288.p;…
12 …Parent=rna-NW_004929286.1:1559..3530;Name=GNOMON:229039288.p;gbkey=CDS;product=GNOMON:229039288.p;…
H A Drw-568-4.entry.gff311 GU182347.1 Genbank exon 1186 1221 . + . ID=exon-KIR3DL3-2;Parent=rna-KIR3DL3;gbkey=mRNA;gene=KIR3DL…
12 GU182347.1 Genbank exon 1992 2276 . + . ID=exon-KIR3DL3-3;Parent=rna-KIR3DL3;gbkey=mRNA;gene=KIR3DL…
13 GU182347.1 Genbank exon 3550 3849 . + . ID=exon-KIR3DL3-4;Parent=rna-KIR3DL3;gbkey=mRNA;gene=KIR3DL…
99 GU182347.1 Genbank mRNA 75429 87779 . + . ID=rna-KIR2DP1;Parent=gene-KIR2DP1;gbkey=mRNA;gene=KIR2DP…
100 GU182347.1 Genbank exon 75429 75462 . + . ID=exon-KIR2DP1-1;Parent=rna-KIR2DP1;gbkey=mRNA;gene=KIR2…
101 GU182347.1 Genbank exon 76520 76555 . + . ID=exon-KIR2DP1-2;Parent=rna-KIR2DP1;gbkey=mRNA;gene=KIR2…
102 GU182347.1 Genbank exon 77281 77562 . + . ID=exon-KIR2DP1-3;Parent=rna-KIR2DP1;gbkey=mRNA;gene=KIR2…
103 GU182347.1 Genbank exon 79016 79314 . + . ID=exon-KIR2DP1-4;Parent=rna-KIR2DP1;gbkey=mRNA;gene=KIR2…
104 GU182347.1 Genbank exon 80838 81131 . + . ID=exon-KIR2DP1-5;Parent=rna-KIR2DP1;gbkey=mRNA;gene=KIR2…
105 GU182347.1 Genbank exon 84299 84349 . + . ID=exon-KIR2DP1-6;Parent=rna-KIR2DP1;gbkey=mRNA;gene=KIR2…
[all …]
H A Drw-310.entry.gff356 LK023325.1 EMBL mRNA 9651 10618 . + . ID=rna-LRAMOSA09754;Parent=gene-LRAMOSA09754;gbkey=mRNA;locus…
57 LK023325.1 EMBL exon 9651 9681 . + . ID=exon-LRAMOSA09754-1;Parent=rna-LRAMOSA09754;gbkey=mRNA;locu…
58 LK023325.1 EMBL exon 9682 9857 . + . ID=exon-LRAMOSA09754-2;Parent=rna-LRAMOSA09754;gbkey=mRNA;locu…
59 LK023325.1 EMBL exon 9910 10018 . + . ID=exon-LRAMOSA09754-3;Parent=rna-LRAMOSA09754;gbkey=mRNA;loc…
60 LK023325.1 EMBL exon 10102 10299 . + . ID=exon-LRAMOSA09754-4;Parent=rna-LRAMOSA09754;gbkey=mRNA;lo…
61 LK023325.1 EMBL exon 10372 10500 . + . ID=exon-LRAMOSA09754-5;Parent=rna-LRAMOSA09754;gbkey=mRNA;lo…
62 LK023325.1 EMBL exon 10501 10618 . + . ID=exon-LRAMOSA09754-6;Parent=rna-LRAMOSA09754;gbkey=mRNA;lo…
82 LK023325.1 EMBL mRNA 21891 23019 . + . ID=rna-LRAMOSA09756;Parent=gene-LRAMOSA09756;gbkey=mRNA;locu…
83 LK023325.1 EMBL exon 21891 21930 . + . ID=exon-LRAMOSA09756-1;Parent=rna-LRAMOSA09756;gbkey=mRNA;lo…
84 LK023325.1 EMBL exon 21992 23019 . + . ID=exon-LRAMOSA09756-2;Parent=rna-LRAMOSA09756;gbkey=mRNA;lo…
[all …]
H A Drw-568-1.entry.gff330 NW_004504305.1 BestRefSeq exon 12951 13300 . - . ID=exon-NM_002490.4-1;Parent=rna-NM_002490.4;Dbxre…
31 NW_004504305.1 BestRefSeq exon 9405 9520 . - . ID=exon-NM_002490.4-2;Parent=rna-NM_002490.4;Dbxref=…
32 NW_004504305.1 BestRefSeq exon 7871 8659 . - . ID=exon-NM_002490.4-3;Parent=rna-NM_002490.4;Dbxref=…
47 NW_004504305.1 Gnomon exon 45824 45910 . - . ID=exon-XR_001756670.1-1;Parent=rna-XR_001756670.1;Dbx…
48 NW_004504305.1 Gnomon exon 44510 44885 . - . ID=exon-XR_001756670.1-2;Parent=rna-XR_001756670.1;Dbx…
146 NW_004504305.1 Gnomon exon 54481 54520 . + . ID=exon-XR_952539.2-1;Parent=rna-XR_952539.2;Dbxref=Ge…
147 NW_004504305.1 Gnomon exon 58531 59046 . + . ID=exon-XR_952539.2-2;Parent=rna-XR_952539.2;Dbxref=Ge…
148 NW_004504305.1 Gnomon exon 59359 59891 . + . ID=exon-XR_952539.2-3;Parent=rna-XR_952539.2;Dbxref=Ge…
149 NW_004504305.1 Gnomon exon 70687 71202 . + . ID=exon-XR_952539.2-4;Parent=rna-XR_952539.2;Dbxref=Ge…
150 NW_004504305.1 Gnomon exon 71515 73413 . + . ID=exon-XR_952539.2-5;Parent=rna-XR_952539.2;Dbxref=Ge…
[all …]
H A Dmss-346.bioseq.asn37 data rna {
47 data rna {
98 data rna {
108 data rna {
118 data rna {
166 data rna {
176 data rna {
186 data rna {
240 data rna {
250 data rna {
[all …]
H A Drw-568-2.entry.gff315 AE014135.4 Genbank CDS 930 1079 . + 0 ID=cds-EDP27932.2;Parent=rna-gnl|FlyBase|CG45760-RB;Dbxref=FL…
16 AE014135.4 Genbank CDS 1144 1410 . + 0 ID=cds-EDP27932.2;Parent=rna-gnl|FlyBase|CG45760-RB;Dbxref=F…
17 AE014135.4 Genbank CDS 1768 3851 . + 0 ID=cds-EDP27932.2;Parent=rna-gnl|FlyBase|CG45760-RB;Dbxref=F…
18 AE014135.4 Genbank CDS 4353 4527 . + 1 ID=cds-EDP27932.2;Parent=rna-gnl|FlyBase|CG45760-RB;Dbxref=F…
19 AE014135.4 Genbank CDS 4592 4824 . + 0 ID=cds-EDP27932.2;Parent=rna-gnl|FlyBase|CG45760-RB;Dbxref=F…
20 AE014135.4 Genbank CDS 4875 4995 . + 1 ID=cds-EDP27932.2;Parent=rna-gnl|FlyBase|CG45760-RB;Dbxref=F…
2353 AE014135.4 Genbank miRNA 400705 400724 . - . ID=rna-gnl|FlyBase|CR46291-RB;Parent=rna-gnl|FlyBase|C…
2355 AE014135.4 Genbank miRNA 400746 400765 . - . ID=rna-gnl|FlyBase|CR46291-RA;Parent=rna-gnl|FlyBase|C…
2523 AE014135.4 Genbank CDS 466501 466669 . - 0 ID=cds-AAF59342.1;Parent=rna-gnl|FlyBase|CG2009-RA;Dbxre…
2524 AE014135.4 Genbank CDS 464797 465315 . - 2 ID=cds-AAF59342.1;Parent=rna-gnl|FlyBase|CG2009-RA;Dbxre…
[all …]
H A Drw-234.annot.gff35 U00096.3 Genbank antisense_RNA 190 199 . + . ID=rna-MSS635_000001;Parent=gene-MSS635_000001;Dbxref=…
6 U00096.3 Genbank exon 190 199 . + . ID=exon-MSS635_000001-1;Parent=rna-MSS635_000001;Dbxref=EcoGene…
7 U00096.3 Genbank antisense_RNA 200 209 . + . ID=rna-MSS635_000001-2;Parent=gene-MSS635_000001;Dbxre…
8 U00096.3 Genbank exon 200 209 . + . ID=exon-MSS635_000001-2-1;Parent=rna-MSS635_000001-2;Dbxref=Eco…
9 U00096.3 Genbank ncRNA 210 219 . + . ID=rna-MSS635_000001-3;Parent=gene-MSS635_000001;Dbxref=EcoGen…
10 U00096.3 Genbank exon 210 219 . + . ID=exon-MSS635_000001-3-1;Parent=rna-MSS635_000001-3;Dbxref=Eco…
11 U00096.3 Genbank lnc_RNA 220 229 . + . ID=rna-MSS635_000001-4;Parent=gene-MSS635_000001;Dbxref=EcoG…
12 U00096.3 Genbank exon 220 229 . + . ID=exon-MSS635_000001-4-1;Parent=rna-MSS635_000001-4;Dbxref=Eco…
/dports/biology/jalview/jalview/src/jalview/gui/
H A DAppVarna.java115 _lastRNAhighlighted = rna; in VarnaHighlighter()
139 _lastRNAhighlighted = rna; in highlightRegion()
402 if (rna == null) in mouseOverSequence()
427 if (rna == null) in selection()
633 rna = trimRNA(rna, modelName); in addModel()
635 models.put(rna, new RnaModel(modelName, model.ann, model.seq, rna, in addModel()
637 vab.addStructure(rna); in addModel()
638 return rna; in addModel()
726 RNA rna = fromSession.rna; in addModelSession() local
734 models.put(rna, newModel); in addModelSession()
[all …]
H A DAppVarnaBinding.java65 import fr.orsay.lri.varna.models.rna.RNA;
182 return selected.rna; in getSelectedRNA()
442 public String getStateInfo(RNA rna) in getStateInfo() argument
460 if (model.rna == rna) in getStateInfo()
486 vp.showRNA(sel.rna, sel.config); in getStateInfo()
522 vp.showRNA(sel.rna, sel.config); in showSelectedStructure()
546 public void addStructure(RNA rna) in addStructure() argument
549 addStructure(rna, config); in addStructure()
558 drawRna(rna, config); in addStructure()
559 _rnaList.add(config, rna, rna.getName()); in addStructure()
[all …]
/dports/science/lammps/lammps-stable_29Sep2021/src/YAFF/
H A Dimproper_distharm.cpp132 xna *= rna; in compute()
133 yna *= rna; in compute()
134 zna *= rna; in compute()
151 f2[0] = a*( yad*zcd - zad*ycd )*rna + a*da*rna*( yna*zcd - zna*ycd); in compute()
152 f2[1] = a*( zad*xcd - xad*zcd )*rna + a*da*rna*( zna*xcd - xna*zcd); in compute()
153 f2[2] = a*( xad*ycd - yad*xcd )*rna + a*da*rna*( xna*ycd - yna*xcd); in compute()
155 f3[0] = - a*( yad*zcd - zad*ycd )*rna - a*da*rna*( yna*zcd - zna*ycd); in compute()
156 f3[1] = - a*( zad*xcd - xad*zcd )*rna - a*da*rna*( zna*xcd - xna*zcd); in compute()
162 f4[0] += a*( yad*zbc - zad*ybc )*rna + a*da*rna*( yna*zbc - zna*ybc); in compute()
163 f4[1] += a*( zad*xbc - xad*zbc )*rna + a*da*rna*( zna*xbc - xna*zbc); in compute()
[all …]
H A Dimproper_sqdistharm.cpp132 xna *= rna; in compute()
133 yna *= rna; in compute()
134 zna *= rna; in compute()
150 f2[0] = a*( yad*zcd - zad*ycd )*rna + a*da*rna*( yna*zcd - zna*ycd); in compute()
151 f2[1] = a*( zad*xcd - xad*zcd )*rna + a*da*rna*( zna*xcd - xna*zcd); in compute()
152 f2[2] = a*( xad*ycd - yad*xcd )*rna + a*da*rna*( xna*ycd - yna*xcd); in compute()
154 f3[0] = - a*( yad*zcd - zad*ycd )*rna - a*da*rna*( yna*zcd - zna*ycd); in compute()
155 f3[1] = - a*( zad*xcd - xad*zcd )*rna - a*da*rna*( zna*xcd - xna*zcd); in compute()
161 f4[0] += a*( yad*zbc - zad*ybc )*rna + a*da*rna*( yna*zbc - zna*ybc); in compute()
162 f4[1] += a*( zad*xbc - xad*zbc )*rna + a*da*rna*( zna*xbc - xna*zbc); in compute()
[all …]
/dports/science/lammps/lammps-stable_29Sep2021/src/EXTRA-MOLECULE/
H A Dimproper_distance.cpp126 xna *= rna; in compute()
127 yna *= rna; in compute()
128 zna *= rna; in compute()
142 …[0] = a*( -xna -yab*(zbd-zbc)*rna +zab*(ybd-ybc)*rna -da*( -yna*(zbd-zbc) + zna*(ybd… in compute()
143 …f2[1] = a*( +xab*(zbd-zbc)*rna -yna +zab*(xbc-xbd)*rna -da*( +xna*(zbd-zbc) + zna*(x… in compute()
144 …f2[2] = a*( -xab*(ybd-ybc)*rna -yab*(xbc-xbd)*rna -zna -da*( +xna*(ybc-ybd) - yna*(x… in compute()
146 f3[0] = a*( ( yab*zbd -zab*ybd ) *rna +da*( -yna*zbd +zna*ybd )*rna); in compute()
147 f3[1] = a*( ( -xab*zbd +zab*xbd ) *rna +da*( +xna*zbd -zna*xbd )*rna); in compute()
148 f3[2] = a*( ( +xab*ybd -yab*xbd ) *rna +da*( -xna*ybd +yna*xbd )*rna); in compute()
150 f4[0] = a*( ( -yab*zbc +zab*ybc ) *rna -da*( -yna*zbc +zna*ybc )*rna); in compute()
[all …]
/dports/security/libgcrypt/libgcrypt-1.9.4/cipher/
H A Drijndael-aarch64.S92 eor rna, rna, RT0; \
115 eor rna, rna, rd, ror #8; \
127 eor rna, rna, RT2, ror #16; \
136 eor rna, rna, RT1, ror #24; \
170 orr rna, rna, rd, ror #8; \
181 orr rna, rna, RT2, ror #16; \
191 orr rna, rna, RT1, ror #24; \
315 eor rna, rna, RT0; \
338 eor rna, rna, rb, ror #8; \
350 eor rna, rna, RT2, ror #16; \
[all …]
H A Drijndael-arm.S97 eor rna, rna, RT0; \
120 eor rna, rna, rd, ror #8; \
132 eor rna, rna, RT2, ror #16; \
141 eor rna, rna, RT1, ror #24; \
175 orr rna, rna, rd, ror #8; \
186 orr rna, rna, RT2, ror #16; \
196 orr rna, rna, RT1, ror #24; \
352 eor rna, rna, RT0; \
375 eor rna, rna, rb, ror #8; \
387 eor rna, rna, RT2, ror #16; \
[all …]
/dports/mail/thunderbird/thunderbird-91.8.0/comm/third_party/libgcrypt/cipher/
H A Drijndael-aarch64.S92 eor rna, rna, RT0; \
115 eor rna, rna, rd, ror #8; \
127 eor rna, rna, RT2, ror #16; \
136 eor rna, rna, RT1, ror #24; \
170 orr rna, rna, rd, ror #8; \
181 orr rna, rna, RT2, ror #16; \
191 orr rna, rna, RT1, ror #24; \
315 eor rna, rna, RT0; \
338 eor rna, rna, rb, ror #8; \
350 eor rna, rna, RT2, ror #16; \
[all …]
H A Drijndael-arm.S97 eor rna, rna, RT0; \
120 eor rna, rna, rd, ror #8; \
132 eor rna, rna, RT2, ror #16; \
141 eor rna, rna, RT1, ror #24; \
175 orr rna, rna, rd, ror #8; \
186 orr rna, rna, RT2, ror #16; \
196 orr rna, rna, RT1, ror #24; \
352 eor rna, rna, RT0; \
375 eor rna, rna, rb, ror #8; \
387 eor rna, rna, RT2, ror #16; \
[all …]
/dports/science/plumed/plumed2-2.7.2/user-doc/tutorials/old_tutorials/trieste-1/.solutions/
H A Dplumed-ex2.dat7 rna: GROUP ATOMS=1-258
12 WHOLEMOLECULES ENTITY0=rna
16 DUMPATOMS ATOMS=rna FILE=rna-whole.gro
20 FIT_TO_TEMPLATE REFERENCE=ref-rna.pdb TYPE=OPTIMAL
25 DUMPATOMS ATOMS=rna FILE=rna-aligned.gro
32 DUMPATOMS ATOMS=rna,mg FILE=rna-select.gro
36 center: CENTER ATOMS=rna
43 DUMPATOMS ATOMS=rna,wat,mg FILE=rna-wrap.gro
/dports/biology/viennarna/ViennaRNA-2.4.18/packaging/debian/
H A Dcontrol12 Replaces: vienna-rna (<< 2.2.1-2)
13 Breaks: vienna-rna (<< 2.2.1-2)
14 Recommends: python-rna, perl-rna
23 Conflicts: vienna-rna (<< 2.2.1-2)
31 Conflicts: vienna-rna (<< 2.2.1-2)
35 Package: python-rna
38 Conflicts: vienna-rna (<< 2.2.1-2)
44 Package: python3-rna
47 Conflicts: vienna-rna (<< 2.2.1-2)
53 Package: perl-rna
[all …]
/dports/biology/p5-Bio-Variation/Bio-Variation-1.7.5/t/
H A DAAReverseMutate.t41 my $rna = pop @points;
42 isa_ok($rna, 'Bio::Variation::RNAChange');
44 is $rna->length, 1;
45 is $rna->allele_ori->seq, 't';
46 is $rna->allele_mut->seq, 'c';
48 is $rna->codon_ori, 'ttc', "Codon_ori is |". $rna->codon_ori. "|";
50 is $rna->codon_pos, 2;
/dports/biology/jalview/jalview/src/jalview/datamodel/
H A DSecondaryStructureAnnotation.java23 import fr.orsay.lri.varna.models.rna.RNA;
30 public SecondaryStructureAnnotation(RNA rna) in SecondaryStructureAnnotation() argument
32 super("Secondary Structure", "Un truc trop cool", getAnnotation(rna)); in SecondaryStructureAnnotation()
34 _rna = rna; in SecondaryStructureAnnotation()
42 public static Annotation[] getAnnotation(RNA rna) in getAnnotation() argument
44 Annotation[] ann = new Annotation[rna.getSize()]; in getAnnotation()
/dports/biology/py-biopython/biopython-1.79/Tests/
H A Dtest_translate.py18 rna = dna.transcribe()
19 self.assertEqual(rna, "AUA")
22 rna = dna.transcribe()
24 rna,
28 rna = Seq.Seq(s)
29 dna = rna.back_transcribe()
76 rna = Seq.Seq(r)
77 protein = rna.translate(to_stop=True)
79 gapped_protein = rna.translate()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/gff3reader_test_cases/
H A Dgff2-moltypes.asn22 data rna {
40 data rna {
58 data rna {
76 data rna {
94 data rna {
112 data rna {
130 data rna {
148 data rna {
166 data rna {
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/gff3reader_test_cases_genbank/
H A Dgff2-moltypes.asn22 data rna {
40 data rna {
58 data rna {
76 data rna {
94 data rna {
112 data rna {
130 data rna {
148 data rna {
166 data rna {

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