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/dports/biology/exonerate/exonerate-2.4.0/src/util/
H A Dfastaannotatecdna.c34 cdna->id, in find_translation()
35 Sequence_get_strand_as_char(cdna), in find_translation()
60 while((cdna = FastaDB_next(cdna_fdb, mask))){ in fastaannotatecdna()
64 protein_path, cdna->seq->id); in fastaannotatecdna()
68 if((protein->seq->len*3) > cdna->seq->len) in fastaannotatecdna()
71 cdna->seq->id, cdna->seq->len); in fastaannotatecdna()
77 rc_seq = Sequence_revcomp(cdna->seq); in fastaannotatecdna()
89 FastaDB_Seq_destroy(cdna); in fastaannotatecdna()
91 cdna = protein = NULL; in fastaannotatecdna()
93 if(cdna) in fastaannotatecdna()
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/dports/lang/slib/slib-3b6/
H A Dncbi-dna.txi19 @defun mrna<-cdna str
25 @defun codons<-cdna cdna
28 sequence encoded by @var{cdna} starting with its first occurence of
33 @defun protein<-cdna cdna
36 encoded by @var{cdna} starting with its first occurence of @samp{atg}.
40 @defun p<-cdna cdna
43 sequence encoded by @var{cdna} starting with its first occurence of
53 @defun cdna:base-count cdna
56 @samp{t} occurrencing in @var{cdna}.
60 @defun cdna:report-base-count cdna
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/dports/biology/wise/wise2.4.1/src/dynlibsrc/
H A Dcdna.xs6 truncate_cDNA(cdna,start,stop)
7 Wise2_cDNA * cdna
28 cDNA_name(cdna)
29 Wise2_cDNA * cdna
31 RETVAL = Wise2_cDNA_name(cdna);
38 cDNA_length(cdna)
39 Wise2_cDNA * cdna
41 RETVAL = Wise2_cDNA_length(cdna);
48 cDNA_seqchar(cdna,pos)
49 Wise2_cDNA * cdna
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H A Dcdna.dy32 #include "cdna.h"
40 It does not alter cdna, rather it returns a new
43 cdna r cDNA that is truncated
45 cDNA * truncate_cDNA(cDNA * cdna,int start,int stop)
115 char * cDNA_name(cDNA * cdna)
117 return cdna->baseseq->name;
124 int cDNA_length(cDNA * cdna)
126 return cdna->baseseq->len;
132 cdna cDNA
135 char cDNA_seqchar(cDNA * cdna,int pos)
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H A Dcdna.tex1 \section{cdna} section in File Documentation
33 \item[cdna] [READ ] cDNA that is truncated [cDNA *]
42 It does not alter cdna, rather it returns a new
67 \item[External C] {\tt Wise2_cDNA_name (cdna)}
68 \item[Perl] {\tt &Wise2::cDNA::cDNA_name (cdna)}
75 \item[cdna] [UNKN ] Undocumented argument [cDNA *]
84 \item[External C] {\tt Wise2_cDNA_length (cdna)}
85 \item[Perl] {\tt &Wise2::cDNA::cDNA_length (cdna)}
92 \item[cdna] [UNKN ] Undocumented argument [cDNA *]
101 \item[External C] {\tt Wise2_cDNA_seqchar (cdna,pos)}
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H A Dcdna.c25 cDNA * truncate_cDNA(cDNA * cdna,int start,int stop) in truncate_cDNA() argument
27 return cDNA_from_Sequence(magic_trunc_Sequence(cdna->baseseq,start,stop)); in truncate_cDNA()
126 char * cDNA_name(cDNA * cdna) in cDNA_name() argument
128 return cdna->baseseq->name; in cDNA_name()
142 int cDNA_length(cDNA * cdna) in cDNA_length() argument
144 return cdna->baseseq->len; in cDNA_length()
159 char cDNA_seqchar(cDNA * cdna,int pos) in cDNA_seqchar() argument
161 return cdna->baseseq->seq[pos]; in cDNA_seqchar()
H A Dcdna.pod3 cdna module - part of the Wise2 package
38 &Wise2::cDNA::truncate_cDNA(cdna,start,stop)
43 It does not alter cdna, rather it returns a new
48 Argument cdna [READ ] cDNA that is truncated [cDNA *]
69 &Wise2::cDNA::cDNA_name(cdna)
75 Argument cdna [UNKN ] Undocumented argument [cDNA *]
81 &Wise2::cDNA::cDNA_length(cdna)
87 Argument cdna [UNKN ] Undocumented argument [cDNA *]
93 &Wise2::cDNA::cDNA_seqchar(cdna,pos)
99 Argument cdna [UNKN ] cDNA [cDNA *]
H A Dcdna_api.h36 Wise2_cDNA * Wise2_truncate_cDNA( Wise2_cDNA * cdna,int start,int stop);
61 char * Wise2_cDNA_name( Wise2_cDNA * cdna);
73 int Wise2_cDNA_length( Wise2_cDNA * cdna);
86 char Wise2_cDNA_seqchar( Wise2_cDNA * cdna,int pos);
H A Dcdna.h50 cDNA * Wise2_truncate_cDNA(cDNA * cdna,int start,int stop);
125 char * Wise2_cDNA_name(cDNA * cdna);
139 int Wise2_cDNA_length(cDNA * cdna);
154 char Wise2_cDNA_seqchar(cDNA * cdna,int pos);
/dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/lib/Bio/Tools/Run/Alignment/
H A DSim4.pm241 my ($self,$cdna,$genomic) = @_;
243 $self->cdna_seq($cdna) if $cdna;
320 my ($self, $cdna,$genomic) = @_;
326 if(ref($cdna)) {
327 my @cdna = ref $cdna eq "ARRAY" ? @{$cdna} : ($cdna);
330 foreach my $c (@cdna){
337 if($#cdna > 0){
342 my $sio = Bio::SeqIO->new(-file=>$cdna,-format=>"fasta");
348 $cdna_file = $cdna;
/dports/biology/wise/wise2.4.1/src/test/
H A Dshort.test10 name basic-cdna
11 desc cdna test case (protein v cdna), all outputs
17 do genewise short.pep short.dna -pretty -para -genes -sum -cdna -trans -ace -gener -alb -pal -qu…
20 name hmm-binary-cdna
21 desc cdna test case (protein v cdna), all outputs
36 desc cdna test case (protein v cdna), all outputs
37 do genewise -init local HMM.ascii -hmmer short.dna -pretty -para -genes -sum -cdna -trans -ace …
42 do genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init gl…
47 do genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init gl…
/dports/biology/wise/wise2.4.1/src/models/
H A Destwise.c26 cDNA * cdna = NULL; variable
217 free_cDNA(cdna); in free_io_objects()
228 free_cDNA(cdna); in reverse_target()
230 cdna = cd_temp; in reverse_target()
304 tend = cdna->baseseq->len; in build_objects()
310 free_cDNA(cdna); in build_objects()
311 cdna = cdna_temp; in build_objects()
322 free_cDNA(cdna); in build_objects()
323 cdna = cdna_temp; in build_objects()
327 cdna->baseseq->offset = 1; in build_objects()
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H A Dpseudowise.c89 if( cdna->seq[pep_pos*3] != gen->seq[gen_pos] || in pseudo_gene_assessment()
90 cdna->seq[pep_pos*3+1] != gen->seq[gen_pos+1] || in pseudo_gene_assessment()
91 cdna->seq[pep_pos*3+2] != gen->seq[gen_pos+2] ) { in pseudo_gene_assessment()
121 assert(cdna); in check_pep_cdna_synchrony()
124 if( ! (is_dna_SequenceType(cdna->type)) ) { in check_pep_cdna_synchrony()
129 if( pep->seq[i] != aminoacid_from_seq(ct,cdna->seq+(i*3)) ) { in check_pep_cdna_synchrony()
147 Sequence * cdna = NULL; in main() local
212 cdna = read_fasta_file_Sequence(argv[2]); in main()
215 if( prot == NULL || cdna == NULL || genomic == NULL ) { in main()
220 offset = check_pep_cdna_synchrony(cdna,prot,ct); in main()
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H A Destwrap.xs28 AlnBlock_from_Protein_estwise_wrap(pro,cdna,cp,cm,ct,comp,gap,ext,is_global,rmd,alg,rm,use_syn,allN…
30 Wise2_cDNA * cdna
45 …RETVAL = Wise2_AlnBlock_from_Protein_estwise_wrap(pro,cdna,cp,cm,ct,comp,gap,ext,is_global,rmd,alg…
52 AlnBlock_from_TSM_estwise_wrap(tsm,cdna,cp,cm,ct,rmd,alg,use_syn,force_flat_insert,allN,dpri)
54 Wise2_cDNA * cdna
65 …RETVAL = Wise2_AlnBlock_from_TSM_estwise_wrap(tsm,cdna,cp,cm,ct,rmd,alg,use_syn,force_flat_insert,…
H A Destwrap.tex35 \item[External C] {\tt Wise2_AlnBlock_from_Protein_estwise_wrap (pro,cdna,cp,cm,ct,comp,gap,ext,is_…
36 \item[Perl] {\tt &Wise2::AlnBlock_from_Protein_estwise_wrap (pro,cdna,cp,cm,ct,comp,gap,ext,is_glob…
42 \item[cdna] [READ ] cdna to be compared to [cDNA *]
43 \item[cp] [READ ] cdna parser indicating insertion deletion probabilities [cDNAParser *]
69 \item[External C] {\tt Wise2_AlnBlock_from_TSM_estwise_wrap (tsm,cdna,cp,cm,ct,rmd,alg,use_syn,forc…
70 \item[Perl] {\tt &Wise2::AlnBlock_from_TSM_estwise_wrap (tsm,cdna,cp,cm,ct,rmd,alg,use_syn,force_fl…
76 \item[cdna] [READ ] cdna to be compared to [cDNA *]
77 \item[cp] [READ ] cdna parser indicating insertion deletion probabilities [cDNAParser *]
H A Destwrap.pod40 &Wise2::AlnBlock_from_Protein_estwise_wrap(pro,cdna,cp,cm,ct,comp,gap,ext,is_global,rmd,alg,rm,use_…
51 Argument cdna [READ ] cdna to be compared to [cDNA *]
52 …Argument cp [READ ] cdna parser indicating insertion deletion probabilities [cDNAParser …
71 &Wise2::AlnBlock_from_TSM_estwise_wrap(tsm,cdna,cp,cm,ct,rmd,alg,use_syn,force_flat_insert,allN,dpr…
79 Argument cdna [READ ] cdna to be compared to [cDNA *]
80 …Argument cp [READ ] cdna parser indicating insertion deletion probabilities [cDNAParser …
H A Dgenedisplay.tex29 \item[External C] {\tt Wise2_protcdna_ascii_display (alb,protsequence,protname,protoff,cdna,ct,name…
30 \item[Perl] {\tt &Wise2::protcdna_ascii_display (alb,protsequence,protname,protoff,cdna,ct,name,mai…
39 \item[cdna] [UNKN ] cdna of the match [cDNA *]
48 with cdna into ofp with pretty formatting
/dports/biology/wise/wise2.4.1/src/perl/scripts/
H A Dprotestwise.pl39 $cdna = &Wise2::cDNA::cDNA_from_Sequence($seq);
41 if( $cdna == 0 ) {
77 $alb = &Wise2::AlnBlock_from_Protein_estwise_wrap($pro,$cdna,$cp,$cm,$ct,$comp,-12,-2,0,$rmd,$alg,$…
106 $tmp = &Wise2::cDNA::cDNA_seqchar($cdna,$x);
131 $namecdna = $cdna->baseseq()->name();
H A Destwise.pl118 my($i,$ds,$alb,$cdna);
144 $cdna = $cdb->get_entry($ds->target);
145 if( ! $cdna ) {
150 …$alb= &Wise2::AlnBlock_from_Protein_estwise_wrap($pro,$cdna,$cp,$cm,$ct,$comp,-12,-2,0,$rmd,0,$rm,…
151 …isplay($alb,$pro->baseseq->seq,$pro->baseseq->name,$pro->baseseq->offset,$cdna,$ct,15,50,0,STDOUT);
/dports/biology/jalview/jalview/test/jalview/util/
H A DMappingUtilsTest.java228 cdna.setDataset(null); in testMapSequenceGroup_sequences()
276 sg.addSequence(cdna.getSequenceAt(1), false); in testMapSequenceGroup_sequences()
277 sg.addSequence(cdna.getSequenceAt(0), false); in testMapSequenceGroup_sequences()
395 cdna.setDataset(null); in setupMappedAlignments()
426 dnaView = new AlignViewport(cdna); in setupMappedAlignments()
516 AlignmentI cdna = loadAlignment( in testMapSequenceGroup_columns() local
519 cdna.setDataset(null); in testMapSequenceGroup_columns()
570 sg.addSequence(cdna.getSequenceAt(0), false); in testMapSequenceGroup_columns()
600 AlignmentI cdna = loadAlignment( in testMapSequenceGroup_region() local
603 cdna.setDataset(null); in testMapSequenceGroup_region()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/hgvs/test/
H A Dtest_variations.asn15 mol cdna,
129 mol cdna,
229 mol cdna,
505 mol cdna,
626 mol cdna,
746 mol cdna,
866 mol cdna,
987 mol cdna,
1100 mol cdna,
1198 mol cdna,
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/dports/biology/jalview/jalview/src/jalview/appletgui/
H A DSplitFrame.java74 AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport in init() local
83 ssm.addCommandListener(cdna); in init()
120 AlignmentViewport cdna = topFrame.getAlignViewport().getAlignment() in adjustLayout() local
122 AlignmentViewport protein = cdna == topFrame.viewport in adjustLayout()
150 if (protein != null && cdna != null) in adjustLayout()
154 vs.setCharWidth(scale * cdna.getViewStyle().getCharWidth()); in adjustLayout()
/dports/biology/emboss/EMBOSS-6.6.0/emboss/
H A Dserver.biomart19 sequence: "cdna"
62 sequence: "cdna"
105 sequence: "cdna"
148 sequence: "cdna"
191 sequence: "cdna"
235 sequence: "cdna"
277 sequence: "cdna"
320 sequence: "cdna"
363 sequence: "cdna"
406 sequence: "cdna"
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/dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/t/
H A DSim4.t17 my $cdna = test_input_file("sim4_cdna.fa");
19 my @params = (W=>15,K=>17,D=>10,N=>10,cdna_seq=>$cdna,genomic_seq=>$genomic);
38 my $sio = Bio::SeqIO->new(-file=>$cdna,-format=>"fasta");
58 #test with cdna database as file
76 #test with cdna database as object
/dports/biology/gmap/gmap-2020-09-12/src/
H A Dpair.c200 return this->cdna; in Pair_cdna()
607 PUTC(this->cdna,fp); in print_cdna_sequence()
843 new[j].cdna = complCode[(int) old[i].cdna]; in invert_and_revcomp_path()
862 new[j].cdna = complCode[(int) old[i].cdna]; in invert_and_revcomp_path_and_coords()
1038 PUTC(this->cdna,fp); in Pair_print_continuous()
1046 PUTC(this->cdna,fp); in Pair_print_continuous()
1153 PUTC(this->cdna,fp); in Pair_print_continuous_byexon()
1634 this->cdna); in Pair_dump_array()
1674 this->cdna); in Pair_dump_array_stderr()
7483 PUTC(this->cdna,fp); in Pair_print_exons()
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