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/dports/biology/py-biopython/biopython-1.79/Bio/motifs/
H A Dtransfac.py205 motif = Motif(alphabet="ACGT", counts=counts)
206 motif.update(annotations)
207 motif.references = references
208 record.append(motif)
258 for motif in motifs:
265 length = motif.length
268 sequence = motif.degenerate_consensus
269 letters = sorted(motif.alphabet)
280 + [motif.counts[l][i] for l in letters]
287 value = motif.get(key)
[all …]
H A Dmast.py46 for motif in self:
47 if motif.name == key:
48 return motif
77 motif = meme.Motif(record.alphabet)
79 motif.name = str(i + 1)
80 motif.id = motif_tree.get("id")
81 motif.alt_id = motif_tree.get("alt")
82 motif.length = int(motif_tree.get("length"))
84 record.append(motif)
H A Dthresholds.py17 def __init__(self, motif=None, precision=10 ** 3, pssm=None, background=None): argument
20 self.min_score = min(0.0, motif.min_score())
21 self.interval = max(0.0, motif.max_score()) - self.min_score
22 self.n_points = precision * motif.length
23 self.ic = motif.ic()
35 for lo, mo in zip(motif.log_odds(), motif.pwm()):
36 self.modify(lo, mo, motif.background)
/dports/biology/py-bx-python/bx-python-0.8.13/scripts/
H A Dmaf_word_frequency.py34 motif = string.join([text[i: i + motif_len] for text in texts])
35 if motif in big_map:
36 big_map[motif] += 1
38 big_map[motif] = 1
44 for count, motif in items:
45 print("%d\t%0.10f\t%s" % (count, count / total, motif))
/dports/x11-toolkits/lesstif/lesstif-0.95.2/test/extra/Xlab/
H A DRecordAll11 make motif-tests
12 motif=motif
20 echo "Recording for $thistest $motif"
21 ../Xlab/RecordSession $thistest $motif
/dports/math/igraph/igraph-0.9.5/tests/unit/
H A Digraph_motifs_randesu_estimate.out7 Full graph of 50 vertices, motif size 3, sample all, (50 choose 3 = 19600):
10 Full graph of 50 vertices, motif size 3, sample all, cut_prob 0.1 at each level:
13 Full graph of 50 vertices, motif size 3, sample 20:
16 Full graph of 50 vertices, motif size 3, sample first 40:
19 Full graph of 50 vertices, motif size 4, sample 20 (50 choose 4 = 230300:
22 Triangle and a vertex, motif size 4, sample all:
/dports/x11-toolkits/lesstif/lesstif-0.95.2/test/Xm-2.1/print/
H A DMakefile.am33 SUFFIXES= .motif .mo
36 rm -rf *.motif .mo LessTif LessTif.sum LessTif.log site.exp xlab/*.p*
40 motif_TESTS = $(OBJECTS:.o=.motif)
48 test2.motif: test2.mo
51 test4.motif: test4.mo
54 .mo.motif:
57 motif-tests: ${motif_TESTS}
/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/util/PWM/
H A Dmake_seqLogo.Rscript17 motif = t(data)
19 motif = sweep(motif, 2, colSums(motif), '/')
21 p = makePWM(motif)
/dports/biology/vt/vt-0.57721/
H A Dflank_detector.h130 std::string choose_5prime_repeat_unit(std::string& seq, std::string& motif);
136 std::string choose_fuzzy_5prime_repeat_unit(std::string& seq, std::string& motif);
143 std::string choose_3prime_repeat_unit(std::string& seq, std::string& motif);
149 std::string choose_fuzzy_3prime_repeat_unit(std::string& seq, std::string& motif);
156 std::string choose_exact_repeat_unit(std::string& seq, std::string& motif);
166 void polish_repeat_tract_ends(std::string& repeat_tract, std::string& motif, bool debug=false);
176 void compute_purity_score(std::string& repeat_tract, std::string& motif);
H A Dvntr.h51 …std::string motif; //motif … variable
174 static std::string canonicalize2(std::string& motif);
179 static std::string canonicalize(std::string& motif);
187 static int32_t is_periodic(std::string& motif);
192 bool is_aperiodic(std::string& motif);
197 static std::string get_basis(std::string& motif);
202 static std::string get_basis(char* motif, uint32_t n);
/dports/x11-toolkits/lesstif/lesstif-0.95.2/test/Xm-2.1/translations/
H A DMakefile.am22 SUFFIXES = .motif .mo
25 rm -f *.motif .mo
29 motif_TESTS = $(OBJECTS:.o=.motif)
34 .mo.motif:
37 motif-tests: ${motif_TESTS}
/dports/x11-toolkits/lesstif/lesstif-0.95.2/test/Xm/dynamic_drag/
H A DMakefile.am28 SUFFIXES = .motif .mo
31 rm -rf *.motif *.mo LessTif LessTif.sum LessTif.log site.exp xlab/*.p*
35 motif_TESTS = $(PROGRAMS:=.motif)
41 .mo.motif:
44 test1.motif:
47 motif-tests: ${motif_TESTS}
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/unit_test/gff3writer_test_cases/
H A Drw-310.entry.gff310 …ID=rna-LRAMOSA09751;Parent=gene-LRAMOSA09751;gbkey=mRNA;inference=protein motif:InterPro:IPR027417…
11 …=exon-LRAMOSA09751-1;Parent=rna-LRAMOSA09751;gbkey=mRNA;inference=protein motif:InterPro:IPR027417…
26 …ID=rna-LRAMOSA09752;Parent=gene-LRAMOSA09752;gbkey=mRNA;inference=protein motif:InterPro:IPR013740…
27 …=exon-LRAMOSA09752-1;Parent=rna-LRAMOSA09752;gbkey=mRNA;inference=protein motif:InterPro:IPR013740…
28 …=exon-LRAMOSA09752-2;Parent=rna-LRAMOSA09752;gbkey=mRNA;inference=protein motif:InterPro:IPR013740…
29 …=exon-LRAMOSA09752-3;Parent=rna-LRAMOSA09752;gbkey=mRNA;inference=protein motif:InterPro:IPR013740…
33 …ID=rna-LRAMOSA09753;Parent=gene-LRAMOSA09753;gbkey=mRNA;inference=protein motif:InterPro:IPR025887…
34 …=exon-LRAMOSA09753-1;Parent=rna-LRAMOSA09753;gbkey=mRNA;inference=protein motif:InterPro:IPR025887…
35 …=exon-LRAMOSA09753-2;Parent=rna-LRAMOSA09753;gbkey=mRNA;inference=protein motif:InterPro:IPR025887…
36 …=exon-LRAMOSA09753-3;Parent=rna-LRAMOSA09753;gbkey=mRNA;inference=protein motif:InterPro:IPR025887…
[all …]
/dports/x11-toolkits/lesstif/lesstif-0.95.2/test/Xm-2.1/messages/
H A DMakefile.am27 SUFFIXES = .motif .mo
30 rm -f *.motif .mo
34 motif_TESTS = $(OBJECTS:.o=.motif)
39 .mo.motif:
42 motif-tests: ${motif_TESTS}
/dports/biology/viennarna/ViennaRNA-2.4.18/doc/latex/
H A Dgroup__constraints__ligand.tex17 …nd_gaa6ff0113a3a76dc0b8d62961f4e1dfa0}{vrna\+\_\+sc\+\_\+add\+\_\+hi\+\_\+motif}} (\mbox{\hyperlin…
18 …}\small\item\em Add soft constraints for hairpin or interior loop binding motif. \end{DoxyCompactL…
26 {\footnotesize\ttfamily int vrna\+\_\+sc\+\_\+add\+\_\+hi\+\_\+motif (\begin{DoxyParamCaption}\item…
34 Add soft constraints for hairpin or interior loop binding motif.
38 …a1b0cef17fd40466cef5968eaeeff6166}{vrna\+\_\+fold\+\_\+compound\+\_\+t}} the motif is applied to \\
40 {\em seq} & The sequence motif (may be interspaced by \textquotesingle{}\&\textquotesingle{} charac…
42 {\em structure} & The structure motif (may be interspaced by \textquotesingle{}\&\textquotesingle{}…
44 {\em energy} & The free energy of the motif (e.\+g. binding free energy) \\
50 non-\/zero value if application of the motif using soft constraints was successful
53 …}]This function is attached as method {\bfseries{sc\+\_\+add\+\_\+hi\+\_\+motif()}} to objects of …
H A Dligand_8h.tex27 struct \mbox{\hyperlink{structvrna__sc__motif__s}{vrna\+\_\+sc\+\_\+motif\+\_\+s}}
32 …tif__s}{vrna\+\_\+sc\+\_\+motif\+\_\+s}} \mbox{\hyperlink{ligand_8h_a56615bc45d2aa4d6d3326fb74183c…
37 …nd_gaa6ff0113a3a76dc0b8d62961f4e1dfa0}{vrna\+\_\+sc\+\_\+add\+\_\+hi\+\_\+motif}} (\mbox{\hyperlin…
38 …}\small\item\em Add soft constraints for hairpin or interior loop binding motif. \end{DoxyCompactL…
51 …tif__s}{vrna\+\_\+sc\+\_\+motif\+\_\+s}} \mbox{\hyperlink{ligand_8h_a56615bc45d2aa4d6d3326fb74183c…
57 Here is an example that adds a theophylline binding motif. Free energy
66 …vrna\+\_\+sc\+\_\+add\+\_\+hi\+\_\+motif(vc, \char`\"{}\+GAUACCAG\&\+CCCUUGGCAGC\char`\"{}, \char`…
/dports/x11-toolkits/lesstif/lesstif-0.95.2/test/Xm/reptype/
H A DMakefile.am25 SUFFIXES = .motif .mo
28 rm -rf *.motif *.mo LessTif LessTif.sum LessTif.log site.exp xlab/*.p*
32 motif_TESTS = $(OBJECTS:.o=.motif)
37 .mo.motif:
40 motif-tests: ${motif_TESTS}
/dports/x11-toolkits/lesstif/lesstif-0.95.2/test/Xm/screen/
H A DMakefile.am25 SUFFIXES = .motif .mo
29 motif_TESTS = $(OBJECTS:.o=.motif)
34 .mo.motif:
37 motif-tests: ${motif_TESTS}
43 rm -rf *.motif *.mo LessTif LessTif.sum LessTif.log site.exp xlab/*.p*
/dports/x11-toolkits/lesstif/lesstif-0.95.2/test/Xm/tracking/
H A DMakefile.am25 SUFFIXES = .motif .mo
29 motif_TESTS = $(OBJECTS:.o=.motif)
34 .mo.motif:
37 motif-tests: ${motif_TESTS}
43 rm -rf *.motif *.mo LessTif LessTif.sum LessTif.log site.exp xlab/*.p*
/dports/x11-toolkits/lesstif/lesstif-0.95.2/test/Xm/virtualkeys/
H A DMakefile.am25 SUFFIXES = .motif .mo
29 motif_TESTS = $(OBJECTS:.o=.motif)
34 .mo.motif:
37 motif-tests: ${motif_TESTS}
43 rm -rf *.motif *.mo LessTif LessTif.sum LessTif.log site.exp xlab/*.p*
/dports/x11-toolkits/lesstif/lesstif-0.95.2/test/Xm-2.0/rendition/
H A DMakefile.am24 SUFFIXES = .motif .mo
27 rm -rf *.motif *.mo LessTif LessTif.sum LessTif.log site.exp xlab/*.p*
31 motif_TESTS = $(OBJECTS:.o=.motif)
36 .mo.motif:
39 motif-tests: ${motif_TESTS}
/dports/x11-toolkits/lesstif/lesstif-0.95.2/test/Xm/cascadebutton/
H A DMakefile.am26 SUFFIXES = .motif .mo
29 rm -rf *.motif *.mo LessTif LessTif.sum LessTif.log site.exp xlab/*.p*
33 motif_TESTS = $(OBJECTS:.o=.motif)
38 .mo.motif:
41 motif-tests: ${motif_TESTS}
/dports/x11-toolkits/lesstif/lesstif-0.95.2/test/Xm/command/
H A DMakefile.am26 SUFFIXES = .motif .mo
29 rm -rf *.motif *.mo LessTif LessTif.sum LessTif.log site.exp xlab/*.p*
33 motif_TESTS = $(OBJECTS:.o=.motif)
38 .mo.motif:
41 motif-tests: ${motif_TESTS}
/dports/x11-toolkits/lesstif/lesstif-0.95.2/test/Xm/cutpaste/
H A DMakefile.am25 SUFFIXES = .motif .mo
28 rm -rf *.motif *.mo LessTif LessTif.sum LessTif.log site.exp xlab/*.p*
32 motif_TESTS = $(OBJECTS:.o=.motif)
37 .mo.motif:
40 motif-tests: ${motif_TESTS}
/dports/x11-toolkits/lesstif/lesstif-0.95.2/test/Xm/cascadebuttong/
H A DMakefile.am25 SUFFIXES = .motif .mo
28 rm -rf *.motif *.mo LessTif LessTif.sum LessTif.log site.exp xlab/*.p*
32 motif_TESTS = $(OBJECTS:.o=.motif)
37 .mo.motif:
40 motif-tests: ${motif_TESTS}

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