/dports/biology/exonerate/exonerate-2.4.0/src/util/ |
H A D | fastaannotatecdna.c | 34 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() [all …]
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/dports/lang/slib/slib-3b6/ |
H A D | ncbi-dna.txi | 19 @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 [all …]
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/dports/biology/wise/wise2.4.1/src/dynlibsrc/ |
H A D | cdna.xs | 6 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 [all …]
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H A D | cdna.dy | 32 #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) [all …]
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H A D | cdna.tex | 1 \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)} [all …]
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H A D | cdna.c | 25 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()
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H A D | cdna.pod | 3 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 *]
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H A D | cdna_api.h | 36 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);
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H A D | cdna.h | 50 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);
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/dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/lib/Bio/Tools/Run/Alignment/ |
H A D | Sim4.pm | 241 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;
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/dports/biology/wise/wise2.4.1/src/test/ |
H A D | short.test | 10 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…
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/dports/biology/wise/wise2.4.1/src/models/ |
H A D | estwise.c | 26 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() [all …]
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H A D | pseudowise.c | 89 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() [all …]
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H A D | estwrap.xs | 28 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,…
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H A D | estwrap.tex | 35 \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 *]
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H A D | estwrap.pod | 40 &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 …
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H A D | genedisplay.tex | 29 \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
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/dports/biology/wise/wise2.4.1/src/perl/scripts/ |
H A D | protestwise.pl | 39 $cdna = &Wise2::cDNA::cDNA_from_Sequence($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 = $cdna->baseseq()->name();
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H A D | estwise.pl | 118 my($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);
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/dports/biology/jalview/jalview/test/jalview/util/ |
H A D | MappingUtilsTest.java | 228 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() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/hgvs/test/ |
H A D | test_variations.asn | 15 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, [all …]
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/dports/biology/jalview/jalview/src/jalview/appletgui/ |
H A D | SplitFrame.java | 74 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()
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/dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
H A D | server.biomart | 19 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" [all …]
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/dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/t/ |
H A D | Sim4.t | 17 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
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/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | pair.c | 200 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() [all …]
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