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/dports/biology/mmseqs2/MMseqs2-13-45111/src/commons/
H A DMultiParam.cpp9 this->nucleotides = nucleotides; in MultiParam()
16 return SSTR(multiparam.nucleotides); in format()
27 nucleotides = INT_MAX; in MultiParam()
33 nucleotides = INT_MAX; in MultiParam()
37 nucleotides = aminoacids; in MultiParam()
46 nucleotides = FLT_MAX; in MultiParam()
52 nucleotides = FLT_MAX; in MultiParam()
56 nucleotides = aminoacids; in MultiParam()
67 this->nucleotides = strdup(nucleotides); in MultiParam()
93 free(nucleotides); in ~MultiParam()
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H A DMultiParam.h19 T nucleotides; variable
21 MultiParam(T aminoacids, T nucleotides);
28 nucleotides = value;
39 char* nucleotides; variable
41 MultiParam(const char* aminoacids, const char* nucleotides);
44 nucleotides = strdup(par.nucleotides); in MultiParam()
59 if (nucleotides != NULL) {
60 free(nucleotides);
65 nucleotides = strdup(other.nucleotides);
/dports/biology/gmap/gmap-2020-09-12/src/
H A Dmaxent.c99027 if (nucleotides[i] > 0x3) { in hashseq_nucleotides()
99029 i,nucleotides[i],length); in hashseq_nucleotides()
99033 sum = sum*4 + nucleotides[i]; in hashseq_nucleotides()
99104 if (nucleotides[i] > 0x3) { in hashseq_skip_nucleotides()
99106 i,nucleotides[i],length1); in hashseq_skip_nucleotides()
99110 sum = sum*4 + nucleotides[i]; in hashseq_skip_nucleotides()
99115 if (nucleotides[i] > 0x3) { in hashseq_skip_nucleotides()
99117 ,i,nucleotides[i],length2); in hashseq_skip_nucleotides()
99121 sum = sum*4 + nucleotides[i]; in hashseq_skip_nucleotides()
99250 i = nucleotides[DONOR_MODEL_LEFT_MARGIN]*4 + nucleotides[DONOR_MODEL_LEFT_MARGIN + 1]; in score_donor_dinucleotide_nucleotides()
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H A Dmaxent.h17 Maxent_donor_prob_nucleotides (unsigned char *nucleotides);
21 Maxent_donor_logodds_nucleotides (unsigned char *nucleotides);
28 Maxent_acceptor_prob_nucleotides (unsigned char *nucleotides);
32 Maxent_acceptor_logodds_nucleotides (unsigned char *nucleotides);
H A Dgenome.c502 static const char *nucleotides[65536] = variable
9068 memcpy(Buffer,nucleotides[low & 0x0000FFFF],8); in Genome_uncompress_mmap()
9069 memcpy(&(Buffer[8]),nucleotides[low >> 16],8); in Genome_uncompress_mmap()
9071 memcpy(&(Buffer[24]),nucleotides[high >> 16],8); in Genome_uncompress_mmap()
9091 memcpy(Buffer,nucleotides[low & 0x0000FFFF],8); in Genome_uncompress_mmap()
9092 memcpy(&(Buffer[8]),nucleotides[low >> 16],8); in Genome_uncompress_mmap()
9094 memcpy(&(Buffer[24]),nucleotides[high >> 16],8); in Genome_uncompress_mmap()
9187 memcpy(Buffer,nucleotides[low & 0x0000FFFF],8); in Genome_uncompress_memory()
9188 memcpy(&(Buffer[8]),nucleotides[low >> 16],8); in Genome_uncompress_memory()
9210 memcpy(Buffer,nucleotides[low & 0x0000FFFF],8); in Genome_uncompress_memory()
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/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/
H A Dsequence.c69 vc->nucleotides = (vrna_seq_t *)vrna_realloc(vc->nucleotides, in vrna_sequence_add()
72 set_sequence(&(vc->nucleotides[vc->strands]), in vrna_sequence_add()
86 vc->nucleotides[vc->strands - 1].string, in vrna_sequence_add()
298 memmove(vc->nucleotides + i, vc->nucleotides + i + 1, sizeof(vrna_seq_t) * size); in vrna_sequence_remove()
301 vc->nucleotides = in vrna_sequence_remove()
322 free(fc->nucleotides); in vrna_sequence_remove_all()
323 fc->nucleotides = NULL; in vrna_sequence_remove_all()
407 fc->nucleotides = (vrna_seq_t *)vrna_realloc(fc->nucleotides, in vrna_sequence_prepare()
409 fc->nucleotides[0].string = NULL; in vrna_sequence_prepare()
411 fc->nucleotides[0].length = fc->length; in vrna_sequence_prepare()
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/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/fastx_trimmer/
H A Dfastx_trimmer.c123 fastx.nucleotides[keep_last_base] = 0 ; in main()
127 if ( strlen(fastx.nucleotides) < (size_t)keep_first_base ) //sequence too short - remove it in main()
129 for (i=0; i < strlen(fastx.nucleotides)-keep_first_base+1 ; i++) { in main()
130 fastx.nucleotides[i] = fastx.nucleotides[i+keep_first_base-1]; in main()
133 fastx.nucleotides[i] = 0 ; in main()
137 if (strlen(fastx.nucleotides) <= trim_last_bases) in main()
139 i = strlen(fastx.nucleotides) - trim_last_bases; in main()
142 fastx.nucleotides[i] = 0; in main()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/sequences/
H A Dassignment_3_solution.cpp9 String<Dna5> nucleotides = "AGTCGTGNNANCT"; in main() local
13 for (unsigned i = 0; i < length(nucleotides); ++i){ in main()
14 if (nucleotides[i] < 'G') in main()
15 appendValue(lesser, nucleotides[i]); in main()
16 else if (nucleotides[i] > 'G') in main()
17 appendValue(greater, nucleotides[i]); in main()
H A Dassignment_3.cpp9 String<Dna5> nucleotides = "AGTCGTGNNANCT"; in main() local
13 for (unsigned i = 0; i < length(nucleotides); ++i) in main()
15 appendValue(selected, nucleotides[i]); in main()
H A Dassignment_3_solution.cpp.stdout1 Lesser nucleotides: ACAC
2 Greater nucleotides: TTNNNT
/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/fastx_reverse_complement/
H A Dfastx_reverse_complement.c77 int length = strlen(pFASTX->nucleotides); in reverse_complement_fastx()
83 pFASTX->nucleotides[i] = reverse_complement_base ( pFASTX->nucleotides[i] ) ; in reverse_complement_fastx()
89 temp_nuc = pFASTX->nucleotides[i] ; in reverse_complement_fastx()
90 pFASTX->nucleotides[i] = pFASTX->nucleotides[j] ; in reverse_complement_fastx()
91 pFASTX->nucleotides[j] = temp_nuc; in reverse_complement_fastx()
/dports/biology/py-biopython/biopython-1.79/Bio/SeqIO/
H A DNibIO.py114 nucleotides = indices.translate(table)
115 sequence = Seq(nucleotides)
149 nucleotides = bytes(sequence)
155 nucleotides += suffix
156 if not set(nucleotides).issubset(b"ACGTNacgtn"):
158 indices = nucleotides.translate(table)
/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/libfastx/
H A Dfastx.c122 if (strlen(ascii_quality_scores) != strlen(pFASTX->nucleotides)) in convert_ascii_quality_score_line()
124 strlen(ascii_quality_scores), strlen(pFASTX->nucleotides), in convert_ascii_quality_score_line()
163 if (index != strlen(pFASTX->nucleotides)) { in convert_numeric_quality_score_line()
165 index, strlen(pFASTX->nucleotides), pFASTX->input_line_number ); in convert_numeric_quality_score_line()
354 if (fgets(pFASTX->nucleotides, MAX_SEQ_LINE_LENGTH, pFASTX->input) == NULL) in fastx_read_next_record()
358 chomp(pFASTX->nucleotides); in fastx_read_next_record()
361 if (strlen(pFASTX->nucleotides)==0) in fastx_read_next_record()
366 pFASTX->nucleotides,pFASTX->input_line_number); in fastx_read_next_record()
382 if (strlen(temp_qual) == strlen(pFASTX->nucleotides)) { in fastx_read_next_record()
455 rc = fprintf(pFASTX->output, "%s\n", pFASTX->nucleotides); in fastx_write_record()
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/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/fasta_nucleotide_changer/
H A Dfasta_nucleotide_changer.c103 for (i=0; i < strlen(fastx.nucleotides) ; i++) { in main()
104 if ( fastx.nucleotides[i] == nuc_to ) { in main()
108 if ( fastx.nucleotides[i] == nuc_from ) { in main()
109 fastx.nucleotides[i] = nuc_to ; in main()
/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/fastx_clipper/
H A Dfastx_clipper.cpp262 std::string query = std::string(fastx.nucleotides) + std::string( strlen(adapter), 'N' ); in main()
263 std::string target= std::string( strlen(fastx.nucleotides), 'N' ) + std::string(adapter); in main()
265 std::string query = std::string(fastx.nucleotides) ; in main()
285 fastx.nucleotides[i] = 0 ; in main()
296 if (strlen(fastx.nucleotides) < min_length) { // too-short sequence ? in main()
311 …if ( (discard_unknown_bases && strchr(fastx.nucleotides,'N')!=NULL ) ) { // contains unknown bases… in main()
/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/fastx_artifacts_filter/
H A Dfastx_artifacts_filter.c70 if (fastx->nucleotides[i]==0) in artifact_sequence()
74 switch(fastx->nucleotides[i]) in artifact_sequence()
93 __LINE__, fastx->nucleotides[i], i ) ; in artifact_sequence()
/dports/biology/emboss/EMBOSS-6.6.0/emboss/acd/
H A Dfuzznuc.acd27 help: "The standard IUPAC one-letter codes for the nucleotides are
31 Ambiguities are indicated by listing the acceptable nucleotides
35 brackets '{ }' the nucleotides that are not accepted at a given
36 position. For example: {AG} stands for any nucleotides except A
/dports/biology/viennarna/ViennaRNA-2.4.18/tests/data/
H A Drnafold_hc.cmds4 # Force the first 3 nucleotides to be paired
7 # Prohibit nucleotides 6 to 15 from base pairing
/dports/biology/viennarna/ViennaRNA-2.4.18/doc/latex/
H A Dgroup__struct__utils__wuss.tex13 This notation allows for a fine-\/grained annotation of base pairs and unpaired nucleotides, includ…
18 …Unpaired nucleotides that constitute the hairpin loop are indicated by underscores, {\ttfamily \+\…
26 Unpaired nucleotides in multibranch loops are indicated by commas {\ttfamily ,}.
30 …Single stranded nucleotides in the exterior loop, i.\+e. not enclosed by any other pair are denote…
40 …tions usually ignore pseudo-\/knots entirely treating them as unpaired nucleotides, if not stated …
74 …reats pseudo-\/knots annotated by matching pairs of upper/lowercase letters as unpaired nucleotides
/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/fastq_quality_filter/
H A Dfastq_quality_filter.c118 for (i=0; i< strlen(fastx->nucleotides); i++) { in get_percentile_quality()
143 fprintf(stderr, "%s\n", fastx.nucleotides ) ; in main()
144 for (i=0; i<strlen(fastx.nucleotides); i++) { in main()
/dports/biology/vsearch/vsearch-2.17.1/src/
H A Ddb.cc68 static uint64_t nucleotides = 0; variable
85 nucleotides = new_nucleotides; in db_setinfo()
133 nucleotides = 0; in db_read()
232 nucleotides += sequencelength; in db_read()
363 return nucleotides; in db_getnucleotidecount()
/dports/science/lammps/lammps-stable_29Sep2021/src/CG-DNA/
H A DREADME.md77 pair_oxdna_excv.cpp: excluded volume interaction between the nucleotides
79 pair_oxdna_stk.cpp: stacking interaction between consecutive nucleotides
83 nucleotides on different strands, e.g. A-T and C-G
85 pair_oxdna_xstk.cpp: cross-stacking interaction between nucleotides
87 pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides
/dports/biology/mothur/mothur-1.46.1/source/clearcut/
H A Ddistclearcut.cpp386 long int nucleotides; in NJ_DNA_k2p_correction() local
401 NJ_DNA_count_tt(alignment, i, j, &transitions, &transversions, &nucleotides); in NJ_DNA_k2p_correction()
403 if(!nucleotides) { /* sequences have no non-ambiguous overlap in alignment */ in NJ_DNA_k2p_correction()
407 P = (float)transitions / (float)nucleotides; in NJ_DNA_k2p_correction()
408 Q = (float)transversions / (float)nucleotides; in NJ_DNA_k2p_correction()
/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/fastx_renamer/
H A Dfastx_renamer.c92 strncpy(fastx.name, fastx.nucleotides, sizeof(fastx.name)); in main()
93 strncpy(fastx.name2, fastx.nucleotides, sizeof(fastx.name2)); in main()
/dports/biology/viennarna/ViennaRNA-2.4.18/doc/refman.include/
H A Dio_formats.dox134 For particular nucleotides that are forced to pair, the following @p [ORIENTATION] flags
142 Sequence positions of nucleotides/base pairs are @f$ 1- @f$ based and consist of three
153 Enforces the set of @f$ k @f$ consecutive nucleotides starting at
165 Prohibit a set of @f$ k @f$ consecutive nucleotides to participate
167 @p [WHERE] allows to force the nucleotides to appear within the loop of
175 -# @b "Prohibiting two ranges of nucleotides to pair with each other":\n
184 …This command enforces nucleotides to be unpaired similar to @em prohibiting nucleotides to be pair…
185 as described above. It too marks the corresponding nucleotides to be unpaired, however,
186 the @p [WHERE] flag can be used to enforce specfic loop types the nucleotides must appear in.
212 consecutive nucleotides, starting at position @f$ i @f$. The pseudo free energy is
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