| /dports/biology/emboss/EMBOSS-6.6.0/nucleus/ |
| H A D | embpatlist.c | 272 AjPSeq revseq; in embPatternRegexSearch() local
301 revseq = ajSeqNewSeq(seq); in embPatternRegexSearch()
365 ajSeqDel(&revseq); in embPatternRegexSearch()
403 AjPSeq revseq; in embPatternRegexSearchAll() local
434 revseq = ajSeqNewSeq(seq); in embPatternRegexSearchAll()
507 ajSeqDel(&revseq); in embPatternRegexSearchAll()
538 AjPSeq revseq = NULL; in embPatternSeqSearch() local
571 revseq = ajSeqNewSeq(seq); in embPatternSeqSearch()
652 ajSeqDel(&revseq); in embPatternSeqSearch()
684 AjPSeq revseq = NULL; in embPatternSeqSearchAll() local
[all …]
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| /dports/biology/wise/wise2.4.1/src/models/ |
| H A D | pairwiseshortdna.c | 41 Sequence * revseq; in query_to_reverse_target() local
54 revseq = reverse_complement_Sequence(target); in query_to_reverse_target()
70 assert(revseq); in query_to_reverse_target()
91 no = seq_number_dna_7mer_noN(revseq->seq+i); in query_to_reverse_target()
93 (*sli->add_direct_number)(sli->data,no,revseq,i); in query_to_reverse_target()
125 process_HSP(reverse,query,i,revseq,res_struct,cm); in query_to_reverse_target()
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| H A D | pairwiseshortdna.dy | 51 Sequence * revseq;
64 revseq = reverse_complement_Sequence(target);
80 assert(revseq);
101 no = seq_number_dna_7mer_noN(revseq->seq+i);
103 (*sli->add_direct_number)(sli->data,no,revseq,i);
135 process_HSP(reverse,query,i,revseq,res_struct,cm);
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| /dports/biology/emboss/EMBOSS-6.6.0/doc/programs/master/emboss/apps/inc/ |
| H A D | revseq.usage | 1 Here is a sample session with <b>revseq</b>
9 % <b>revseq tembl:x65923 x65923.rev </b>
24 % <b>revseq tembl:x65923 x65923.rev -norev </b>
39 % <b>revseq tembl:x65923 x65923.rev -nocomp </b>
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| H A D | degapseq.isee | 156 <td><a href="revseq.html">revseq</a></td>
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| H A D | descseq.isee | 156 <td><a href="revseq.html">revseq</a></td>
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| H A D | featmerge.isee | 156 <td><a href="revseq.html">revseq</a></td>
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| H A D | listor.isee | 156 <td><a href="revseq.html">revseq</a></td>
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| H A D | makenucseq.isee | 156 <td><a href="revseq.html">revseq</a></td>
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| H A D | maskambignuc.isee | 156 <td><a href="revseq.html">revseq</a></td>
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| H A D | maskseq.isee | 156 <td><a href="revseq.html">revseq</a></td>
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| /dports/biology/tRNAscan-SE/tRNAscan-SE-2.0/src/ |
| H A D | eufind_main.c | 73 char *seq, *revseq, /* sequence */ in main() local
179 if ((revseq = calloc (sqinfo.len+2, sizeof(char))) == NULL) in main()
181 revcomp(revseq, seq); in main()
183 seq = revseq; in main()
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| H A D | trnascan.c | 1731 char *ptr, *revseq; local
1735 revseq= (char *) calloc (seqlen+1,sizeof(char));
1737 if (revseq == NULL)
1751 revseq[pos]='t';
1754 revseq[pos]='g';
1757 revseq[pos]='c';
1760 revseq[pos]='a';
1763 revseq[pos]='n';
1768 revseq[seqlen] = '\0';
1771 *sequence = revseq;
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| /dports/biology/mafft/mafft-7.267-without-extensions/core/ |
| H A D | makedirectionlist.c | 408 char *tmpseq, *revseq; in main() local
578 revseq = AllocateCharVec( nlenmax+1 ); in main()
628 sreverse( revseq, tmpseq ); in main()
639 seq_grp_nuc( grpseq, revseq ); in main()
738 targ[j].tmpseq = revseq; in main()
761 targ[0].tmpseq = revseq; in main()
795 strcpy( seq[i], revseq ); in main()
821 free( revseq ); in main()
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| /dports/math/iml/iml-1.0.5/src/ |
| H A D | nullspace.c | 117 Pt = revseq(r, n, P); in nullspaceLong()
118 rpt = revseq(r, m, rp); in nullspaceLong()
261 Pt = revseq(r, n, P); in nullspaceMP()
262 rpt = revseq(r, m, rp); in nullspaceMP()
408 Pt = revseq(r, n, P); in kernelLong()
409 rpt = revseq(r, m, rp); in kernelLong()
576 Pt = revseq(r, n, P); in kernelMP()
577 rpt = revseq(r, m, rp); in kernelMP()
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| H A D | certsolve.h | 127 long * revseq (const long r, const long m, const long *A);
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| /dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/pwm/ |
| H A D | pwm_score_maf.py | 105 revseq = pwmx.reverse_complement(subseq)
108 r_score, nill = pwm.score_seq(revseq)[0]
113 rev_score = int(pwmx.match_consensus(revseq, motif))
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| /dports/biology/kallisto/kallisto-0.46.1/src/ |
| H A D | PseudoBam.cpp | 201 revseq(&buf1[0], &buf2[0], s1, q1, slen1); in outputPseudoBam()
265 revseq(&buf1[0], &buf2[0], s2, q2, slen2); in outputPseudoBam()
320 revseq(&buf1[0], &buf2[0], s1, q1, slen1); in outputPseudoBam()
339 void revseq(char *b1, char *b2, const char *s, const char *q, int n) { in revseq() function
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| H A D | PseudoBam.h | 19 void revseq(char *b1, char *b2, const char *s, const char *q, int n);
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| /dports/math/gretl/gretl-2021d/lib/src/ |
| H A D | gretl_join.c | 995 int revseq, in aggr_value() argument
1061 gotit = sub == revseq; in aggr_value()
1066 gotit = sub == revseq; in aggr_value()
1175 int revseq) in handle_midas_setup() argument
1179 series_set_midas_period(jr->l_dset, lv, revseq); in handle_midas_setup()
1181 jr->r_dset->varname[rv], revseq); in handle_midas_setup()
1356 int revseq = 0; in aggregate_data() local
1374 revseq = targvars[0]; in aggregate_data()
1375 jr->midas_m = revseq; in aggregate_data()
1440 zt = aggr_value(jr, &matcher, s, rv, revseq, xmatch, in aggregate_data()
[all …]
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| /dports/biology/trimadap/trimadap-0.1-3-gddfef21/ |
| H A D | ksw.c | 324 static void revseq(int l, uint8_t *s) in revseq() function
348 …revseq(r.qe + 1, copy); revseq(r.te + 1, target); // +1 because qe/te points to the exact end, not… in ksw_align()
351 revseq(r.te + 1, target); in ksw_align()
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| /dports/biology/emboss/EMBOSS-6.6.0/emboss/acd/ |
| H A D | revseq.acd | 1 application: revseq [
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| /dports/www/h2o-devel/h2o-dcc7134/deps/klib/ |
| H A D | ksw.c | 323 static void revseq(int l, uint8_t *s) in revseq() function
344 …revseq(r.qe + 1, query); revseq(r.te + 1, target); // +1 because qe/te points to the exact end, no… in ksw_align()
347 revseq(r.qe + 1, query); revseq(r.te + 1, target); in ksw_align()
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| /dports/biology/checkm/CheckM-1.0.18/scripts/ |
| H A D | evaluatePfamTigrfamHMMs.py | 48 revseq = bioseq.reverse_complement()
51 yield revseq[i:].translate(table)
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| /dports/biology/bwa/bwa-0.7.17/ |
| H A D | ksw.c | 338 static inline void revseq(int l, uint8_t *s) in revseq() function
359 …revseq(r.qe + 1, query); revseq(r.te + 1, target); // +1 because qe/te points to the exact end, no… in ksw_align2()
362 revseq(r.qe + 1, query); revseq(r.te + 1, target); in ksw_align2()
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