> dna<-DNAString("TCTCCCAACCCTTGTACCAGT") > Biostrings::dna2rna(dna) 21-letter "RNAString" instance seq: UCUCCCAACCCUUGUACCAGU > rna<-transcribe(dna) > rna 21-letter "RNAString" instance seq: AGAGGGUUGGGAACAUGGUCA > rna2dna(rna) 21-letter "DNAString" instance seq: AGAGGGTTGGGAACATGGTCA > cD<-cDNA(rna) > cD 21-letter "DNAString" instance seq: TCTCCCAACCCTTGTACCAGT > codons(rna) Views on a 21-letter RNAString subject subject: AGAGGGUUGGGAACAUGGUCA views: start end width [1] 1 3 3 [AGA] [2] 4 6 3 [GGG] [3] 7 9 3 [UUG] [4] 10 12 3 [GGA] [5] 13 15 3 [ACA] [6] 16 18 3 [UGG] [7] 19 21 3 [UCA] > AA<-translate(rna) > AA 7-letter "AAString" instance seq: RGLGTWS > complement(dna) 21-letter "DNAString" instance seq: AGAGGGTTGGGAACATGGTCA > reverseComplement(dna) 21-letter "DNAString" instance seq: ACTGGTACAAGGGTTGGGAGA > reverse(dna) 21-letter "DNAString" instance seq: TGACCATGTTCCCAACCCTCT > library("BSgenome.Hsapiens.UCSC.hg19") Loading required package: BSgenome Loading required package: GenomicRanges > Hsapiens Human genome | | organism: Homo sapiens (Human) | provider: UCSC | provider version: hg19 | release date: Feb. 2009 | release name: Genome Reference Consortium GRCh37 | | single sequences (see '?seqnames'): | chr1 chr2 chr3 | chr4 chr5 chr6 | chr7 chr8 chr9 | chr10 chr11 chr12 | chr13 chr14 chr15 | chr16 chr17 chr18 | chr19 chr20 chr21 | chr22 chrX chrY | chrM chr1_gl000191_random chr1_gl000192_random | chr4_ctg9_hap1 chr4_gl000193_random chr4_gl000194_random | chr6_apd_hap1 chr6_cox_hap2 chr6_dbb_hap3 | chr6_mann_hap4 chr6_mcf_hap5 chr6_qbl_hap6 | chr6_ssto_hap7 chr7_gl000195_random chr8_gl000196_random | chr8_gl000197_random chr9_gl000198_random chr9_gl000199_random | chr9_gl000200_random chr9_gl000201_random chr11_gl000202_random | chr17_ctg5_hap1 chr17_gl000203_random chr17_gl000204_random | chr17_gl000205_random chr17_gl000206_random chr18_gl000207_random | chr19_gl000208_random chr19_gl000209_random chr21_gl000210_random | chrUn_gl000211 chrUn_gl000212 chrUn_gl000213 | chrUn_gl000214 chrUn_gl000215 chrUn_gl000216 | chrUn_gl000217 chrUn_gl000218 chrUn_gl000219 | chrUn_gl000220 chrUn_gl000221 chrUn_gl000222 | chrUn_gl000223 chrUn_gl000224 chrUn_gl000225 | chrUn_gl000226 chrUn_gl000227 chrUn_gl000228 | chrUn_gl000229 chrUn_gl000230 chrUn_gl000231 | chrUn_gl000232 chrUn_gl000233 chrUn_gl000234 | chrUn_gl000235 chrUn_gl000236 chrUn_gl000237 | chrUn_gl000238 chrUn_gl000239 chrUn_gl000240 | chrUn_gl000241 chrUn_gl000242 chrUn_gl000243 | chrUn_gl000244 chrUn_gl000245 chrUn_gl000246 | chrUn_gl000247 chrUn_gl000248 chrUn_gl000249 | | multiple sequences (see '?mseqnames'): | upstream1000 upstream2000 upstream5000 | | (use the '$' or '[[' operator to access a given sequence) > chr22NoN<-mask(Hsapiens$chr22,"N") > alphabetFrequency(Hsapiens$chr22, baseOnly=TRUE) A C G T other 9094775 8375984 8369235 9054551 0 > alphabetFrequency(Hsapiens$chr22) A C G T M R W S 9094775 8375984 8369235 9054551 0 0 0 0 Y K V H D B N - 0 0 0 0 0 0 0 0 + 0 > hasOnlyBaseLetters(Hsapiens$chr22) [1] TRUE > uniqueLetters(Hsapiens$chr22) [1] "A" "C" "G" "T" > GC_content <- letterFrequency(Hsapiens$chr22, letters="CG") > GC_content C|G 16745219 > GC_content <- letterFrequency(Hsapiens$chr22, letters="CG")/letterFrequency(Hsapiens$chr22, letters="ACGT") > GC_content C|G 0.4798807 |
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