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/dports/biology/py-biopython/biopython-1.79/Tests/
H A Dtest_motifs.py613 motif = record[0]
669 motif = record[1]
765 motif = record[0]
1005 motif = record[1]
1197 motif = record[0]
1372 motif = record[1]
1536 motif = record[0]
1540 self.assertEqual(motif.length, 19)
2098 motif = record[0]
2151 motif = record[1]
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/dports/biology/viennarna/ViennaRNA-2.4.18/tests/RNAfold/results/
H A Drnafold.small.cmds.gold4 ud motif 0 detected in MFE structure: [54:56]
5 ud motif 0 detected in MFE structure: [64:66]
8 ud motif 0 detected in centroid structure: [54:56]
10 ud motif 0 detected in MEA structure: [54:56]
11 ud motif 0 detected in MEA structure: [64:66]
16 ud motif 0 detected in MFE structure: [16:18]
21 ud motif 0 detected in MEA structure: [16:18]
33 ud motif 0 detected in MFE structure: [6:8]
34 ud motif 0 detected in MFE structure: [76:78]
40 ud motif 0 detected in MEA structure: [6:8]
[all …]
/dports/math/oleo/oleo-1.99.16/po/
H A Doleo.pot96 #: src/io-motif.c:722
100 #: src/io-motif.c:791
105 #: src/io-motif.c:946 src/io-motif.c:1111
109 #: src/io-motif.c:985 src/io-motif.c:1008 src/io-motif.c:1031
110 #: src/io-motif.c:1053 src/io-motif.c:1070 src/io-motif.c:1955
111 #: src/io-motif.c:3647 src/io-motif.c:3656 src/io-motif.c:3694
112 #: src/io-motif.c:3703 src/io-motif.c:3738 src/io-motif.c:3747
121 #: src/io-motif.c:1436 src/io-motif.c:2927
178 #: src/io-motif.c:3060 src/io-motif.c:5933
217 #: src/io-motif.c:3312 src/io-motif.c:3347
[all …]
H A Den.po100 #: src/io-motif.c:722
105 #: src/io-motif.c:791
110 #: src/io-motif.c:946 src/io-motif.c:1111
114 #: src/io-motif.c:985 src/io-motif.c:1008 src/io-motif.c:1031
115 #: src/io-motif.c:1053 src/io-motif.c:1070 src/io-motif.c:1955
116 #: src/io-motif.c:3647 src/io-motif.c:3656 src/io-motif.c:3694
117 #: src/io-motif.c:3703 src/io-motif.c:3738 src/io-motif.c:3747
126 #: src/io-motif.c:1436 src/io-motif.c:2927
185 #: src/io-motif.c:3060 src/io-motif.c:5933
228 #: src/io-motif.c:3312 src/io-motif.c:3347
[all …]
H A Dfr.po100 #: src/io-motif.c:722
105 #: src/io-motif.c:791
110 #: src/io-motif.c:946 src/io-motif.c:1111
114 #: src/io-motif.c:985 src/io-motif.c:1008 src/io-motif.c:1031
115 #: src/io-motif.c:1053 src/io-motif.c:1070 src/io-motif.c:1955
116 #: src/io-motif.c:3647 src/io-motif.c:3656 src/io-motif.c:3694
117 #: src/io-motif.c:3703 src/io-motif.c:3738 src/io-motif.c:3747
126 #: src/io-motif.c:1436 src/io-motif.c:2927
186 #: src/io-motif.c:3060 src/io-motif.c:5933
231 #: src/io-motif.c:3312 src/io-motif.c:3347
[all …]
H A Dnl.po100 #: src/io-motif.c:722
105 #: src/io-motif.c:791
110 #: src/io-motif.c:946 src/io-motif.c:1111
116 #: src/io-motif.c:985 src/io-motif.c:1008 src/io-motif.c:1031
117 #: src/io-motif.c:1053 src/io-motif.c:1070 src/io-motif.c:1955
118 #: src/io-motif.c:3647 src/io-motif.c:3656 src/io-motif.c:3694
119 #: src/io-motif.c:3703 src/io-motif.c:3738 src/io-motif.c:3747
128 #: src/io-motif.c:1436 src/io-motif.c:2927
189 #: src/io-motif.c:3060 src/io-motif.c:5933
234 #: src/io-motif.c:3312 src/io-motif.c:3347
[all …]
/dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/motif/io/
H A Dtransfac.py5 from bx.motif.pwm import FrequencyMatrix
58 for motif in self:
59 rval[getattr(motif, key)] = motif
103 motif = TransfacMotif()
120 setattr(motif, key, rest)
125 if not getattr(motif, key):
126 setattr(motif, key, [])
135 getattr(motif, key)[k] = v
173 if motif.id or motif.accession or motif.name:
174 return motif
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/dports/biology/py-biopython/biopython-1.79/Bio/motifs/
H A Dpfm.py21 return "\n".join(str(motif) for motif in self)
181 motif.name = motif_name
182 record.append(motif)
194 record.append(motif)
206 record.append(motif)
258 motif.name = motif_name
259 record.append(motif)
269 motif.name = motif_name
270 record.append(motif)
370 record.append(motif)
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H A Dclusterbuster.py19 return "\n".join(str(motif) for motif in self)
38 motif = motifs.Motif(alphabet="GATC", counts=nucleotide_counts)
39 motif.name = motif_name
40 record.append(motif)
59 motif = motifs.Motif(alphabet="GATC", counts=nucleotide_counts)
60 motif.name = motif_name
61 record.append(motif)
H A Dmeme.py122 for motif in self:
123 if motif.name == key:
124 return motif
176 motif = Motif(record.alphabet, instances)
177 motif.id = motif_tree.get("id")
178 motif.name = motif_tree.get("name")
179 motif.alt_id = motif_tree.get("alt")
180 motif.length = int(motif_tree.get("width"))
181 motif.num_occurrences = int(motif_tree.get("sites"))
182 motif.evalue = float(motif_tree.get("e_value"))
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H A Dminimal.py61 motif = motifs.Motif(alphabet=record.alphabet, counts=counts)
62 motif.background = record.background
63 motif.length = length
64 motif.num_occurrences = num_occurrences
65 motif.evalue = evalue
66 motif.name = name
67 record.append(motif)
87 for motif in self:
88 if motif.name == key:
89 return motif
/dports/biology/emboss/EMBOSS-6.6.0/emboss/data/
H A DEmeme.dat1 For each motif that it discovers in the training set, MEME prints the
7 the training set (`sites') of the motif. MEME numbers the motifs
20 the motif, the simplified motif shows the letter probabilities multiplied
36 the motif for database searches. For a motif to be useful for database
43 more than one motif since they can be combined in multiple motif
57 motif 2 in the sample output is:
64 motif. First, the most likely form of the motif can be read from the top
79 motif in BLOCKS format.
87 the motif sites in FASTA format instead of BLOCKS format.
93 by converting the motif letter-probability matrix into a
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/dports/biology/vt/vt-0.57721/
H A Dvntr.cpp38 motif.clear(); in clear()
116 motif==vntr.motif); in equals()
142 std::string cmotif = motif; in canonicalize2()
145 for (uint32_t i=0; i<motif.size(); ++i) in canonicalize2()
169 std::string cmotif = motif; in canonicalize()
171 for (uint32_t i=0; i<motif.size(); ++i) in canonicalize()
196 if (smotif == motif) in is_periodic()
208 bool VNTR::is_aperiodic(std::string& motif) in is_aperiodic() argument
214 if (smotif == motif) in is_aperiodic()
228 return get_basis(const_cast<char*>(motif.c_str()), motif.size()); in get_basis()
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H A Dcandidate_motif_picker.cpp160 char *motif = NULL; in set_motif_from_info_field() local
164 vntr.motif.assign(motif); in set_motif_from_info_field()
165 vntr.basis = vntr.get_basis(vntr.motif); in set_motif_from_info_field()
166 vntr.mlen = vntr.motif.size(); in set_motif_from_info_field()
168 free(motif); in set_motif_from_info_field()
172 vntr.motif = ""; in set_motif_from_info_field()
424 variant.vntr.motif = cm.motif; in next_motif()
454 for (uint32_t i=0; i<motif.size(); ++i) in is_in_indel_fragment()
456 std::string shifted_motif = motif.substr(i) + motif.substr(0,i); in is_in_indel_fragment()
477 for (uint32_t i=0; i<motif.size(); ++i) in choose_repeat_unit()
[all …]
H A Dflank_detector.cpp347 std::string best_motif = motif; in choose_5prime_repeat_unit()
350 int32_t mlen = motif.size(); in choose_5prime_repeat_unit()
375 return motif; in choose_5prime_repeat_unit()
385 std::string best_motif = motif; in choose_fuzzy_5prime_repeat_unit()
388 int32_t mlen = motif.size(); in choose_fuzzy_5prime_repeat_unit()
426 int32_t mlen = motif.size(); in choose_3prime_repeat_unit()
442 return motif; in choose_3prime_repeat_unit()
452 std::string best_motif = motif; in choose_fuzzy_3prime_repeat_unit()
455 int32_t mlen = motif.size(); in choose_fuzzy_3prime_repeat_unit()
538 int32_t mlen = motif.size(); in polish_repeat_tract_ends()
[all …]
H A Dcompute_rl_dist.cpp95 std::string cmotif = motif; in canonicalize()
97 for (uint32_t i=0; i<motif.size(); ++i) in canonicalize()
99 std::string shifted_motif = motif.substr(i) + motif.substr(0,i); in canonicalize()
115 std::string motif = canonicalize(del); in update_stats() local
117 if (stats.find(motif)==stats.end()) in update_stats()
120 stats[motif] = v; in update_stats()
121 stats[motif].resize(rl, 0); in update_stats()
123 ++stats[motif][rl-1]; in update_stats()
134 stats[motif].push_back(0); in update_stats()
151 std::string motif = i->first; in print_dist() local
[all …]
/dports/print/lilypond-devel/lilypond-2.23.5/input/regression/
H A Dmodal-transforms.ly4 \modalInversion work for an octatonic motif."
11 motif = {
21 \motif
22 \modalTranspose c' f' \cOctatonicScale \motif
23 \retrograde \motif
25 \inversion aes' b' \motif
28 s1-"Octatonic motif" |
29 s1-"motif transposed from c to f" |
30 s1-"motif in retrograde" |
31 s1-"motif inverted around aes to b" |
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/dports/print/lilypond/lilypond-2.22.1/input/regression/
H A Dmodal-transforms.ly4 \modalInversion work for an octatonic motif."
11 motif = {
21 \motif
22 \modalTranspose c' f' \cOctatonicScale \motif
23 \retrograde \motif
25 \inversion aes' b' \motif
28 s1-"Octatonic motif" |
29 s1-"motif transposed from c to f" |
30 s1-"motif in retrograde" |
31 s1-"motif inverted around aes to b" |
[all …]
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/magnetism/
H A Djahnteller.py151 motif = "oct"
154 motif = "tet"
157 motif = "unknown"
160 if motif in ["oct", "tet"]:
162 motif = cast(Literal["oct", "tet"], motif) # mypy needs help
193 "motif": motif,
404 if motif in self.spin_configs:
431 if motif == "oct":
438 elif motif == "tet":
463 mu_so_high = JahnTellerAnalyzer.mu_so(species, motif=motif, spin_state="high")
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/dports/converters/wkhtmltopdf/qt-5db36ec/doc/src/widgets-and-layouts/
H A Dgallery-motif.qdoc29 \page gallery-motif.html
50 \o \image motif-checkbox.png
60 \o \image motif-groupbox.png
64 \o \image motif-frame.png
66 \o \image motif-toolbox.png
74 \o \image motif-listview.png
76 \o \image motif-treeview.png
89 \o \image motif-label.png
111 \o \image motif-slider.png
115 \o \image motif-spinbox.png
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/dports/biology/emboss/EMBOSS-6.6.0/doc/programs/master/emboss/apps/inc/
H A Depestfind.output12 Potential PEST motif with 34 amino acids between position 238 and 273.
18 Potential PEST motif with 14 amino acids between position 206 and 221.
24 Poor PEST motif with 18 amino acids between position 363 and 382.
28 Poor PEST motif with 17 amino acids between position 409 and 427.
32 Poor PEST motif with 19 amino acids between position 22 and 42.
36 Poor PEST motif with 10 amino acids between position 440 and 451.
40 Poor PEST motif with 13 amino acids between position 279 and 293.
44 Poor PEST motif with 13 amino acids between position 349 and 363.
48 Invalid PEST motif with 20 amino acids between position 1 and 22.
51 Invalid PEST motif with 13 amino acids between position 43 and 57.
[all …]
/dports/lang/elk/elk-3.99.8/examples/
H A DMakefile.am90 motif/scroll-bar.scm \
91 motif/radio.scm \
93 motif/drawing-area.scm \
94 motif/radio-stuff.scm \
95 motif/popup-menu.scm \
96 motif/pulldown-menu.scm \
97 motif/main-window.scm \
98 motif/menu-stuff.scm \
99 motif/vcr.scm \
100 motif/option-menu.scm \
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/dports/biology/py-biopython/biopython-1.79/Bio/motifs/jaspar/
H A D__init__.py145 for motif in self:
146 dic[motif.matrix_id] = motif
175 motif = motifs[0]
176 counts = motif.counts
216 motif.mask = "*" * motif.length
218 record.append(motif)
243 motif.mask = "*" * motif.length
245 record.append(motif)
329 alphabet = motif.alphabet
330 background = motif.background
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H A Ddb.py139 motif = None
143 return motif
286 num_sites = sum(motif.counts[nt][0] for nt in motif.alphabet)
290 record.append(motif)
389 motif.species = tax_ids
401 motif.acc = accs
410 motif.tf_class = val
418 motif.pazar_id = val
420 motif.medline = val
422 motif.comment = val
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/dports/biology/py-biopython/biopython-1.79/Doc/Tutorial/
H A Dchapter_motifs.tex502 >>> motif.pseudocounts = motifs.jaspar.calculate_pseudocounts(motif)
626 >>> motif = record[0]
639 >>> motif.length
644 >>> motif.name
646 >>> motif.id
766 >>> motif["ID"] # Using motif as a dictionary
1017 in the motif:
1285 >>> print(motif.pwm)
1324 >>> print(motif.pwm)
1400 >>> print("%f" % motif.pssm.mean(motif.background))
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