Function reference • bstringr

bstr/dstr/astr class Class for biological sequences.
`bstr()` `dstr()` `astr()` `is_bstr()` `is_dstr()` `is_astr()` `as_bstr()` `as_astr()` `as_dstr()`	Constructer of the bstr class object
`is_valid_dna_character()`	Detect invalid IUPAC DNA characters
`is_valid_aa_character()`	Detect invalid IUPAC Amino Acid characters
`bstr_rand_seq()` `dstr_rand_seq()` `astr_rand_seq()`	Generate random bstr sequences of desired lengths.
S3 functions for bstr
`c(<bstr>)`	Combine Values into a bstr class object
`[`(<bstr>)	subsetting bstr class object
`sort(<bstr>)`	sort bstr
`print(<bstr>)`	print bstr class object
functions for bstr
`bstr_length()` `dstr_length()` `astr_length()`	Sequence length in the bstr sequences.
`bstr_reverse()` `dstr_reverse()` `astr_reverse()`	Reverse bstr sequence
`bstr_replace()`	Replace matched patterns in bstr sequences by replacements
`bstr_to_upper()` `bstr_to_lower()` `bstr_switch_case()`	Convert case of a bstring sequence.
`bstr_sub()` `bstr_sub<-`() `bstr_sub_replace()`	Extract and replace subsequences from a bstr sequences
`bstr_sub_all()` `bstr_sub_all<-`() `bstr_sub_replace_all()` `bstr_sub_all_replace()`	Extract and replace all subsequences from a bstr sequences
`bstr_remove()` `bstr_remove_num()` `bstr_remove_notalpha()` `bstr_remove_gap()`	Remove all matched patterns in bstr sequences
`bstr_align()`	Align bstr sequence
`bstr_multi_align()`	Align multiple bstr sequence
`bstr_sub_true()`	bstr_sub_true
functions for dstr
`dstr_remove_stop()`	Remove stop codon from DNA sequence
`dstr_complement()` `dstr_complement_fast()`	Return complement sequences
`dstr_rev_comp()` `dstr_rev_comp_fast()`	Return reverse complement sequences
`dstr_find_orf()`	Find open reading frames from DNA
`dstr_find_orf_from_vector()`	Find a main open reading frame from Gataway system vector
`dstr_translate()`	Translate dna -> protein
`dstr_translate_from_vector()`	Find and translate ORF from expression vector
`dstr_align()`	Align dna sequence
`dstr_multi_align()`	Align multiple bstr sequence
`dstr_pcr()`	Calculate PCR product length
`dstr_primer_check()`	Primer check
`dstr_iupac2regex()`	Convert IUPAC CODE to regular expression
`dstr_TOPO()`	Return the product sequence of after TOPO reaction
`dstr_LR()`	Return product sequence after LR reaction
`dstr_TOPO_LR()`	TOPO and LR reaction
Calculate
`calc_GCper()`	Caluculate Oligo GC%
`calc_InFusion_insert_volume()`	Calculate the insert volume for In-Fusion reaction
`calc_InFusion_vector_volume()`	Calculate the vector volume for In-Fusion reaction
`calc_MW_dsDNA()`	Calculate double strand DNA molecular weight
`calc_MW_peptide()`	Calculate protein molecular weight
`calc_MW_ssRNA()`	Calculate single strand RNA molecular weight
`calc_ident()`	calculate % of identical residues
`calc_ident_mat()`	calculate % of identical residues
`calc_oligoDNATm()`	Calculate Oligo DNA Tm
File IO
`read_fasta()`	Read fasta file
`write_fasta()`	write fasta file
`read_genbank()`	Read Genbank file
`write_genbank()`	Write Genbank file
`parse_ACCESSION_FIELD()`	Parse Genbank file ACCESSION FIELD
`parse_DEFINITION_FIELD()`	Parse Genbank file DIFINITION FIELD
`parse_LOCUS_FIELD()`	Parse Genbank file LOCUS FIELD
`parse_ORIGIN_FIELD()`	Parse Genbank file ORIGIN FIELD
`parse_VERSION_FIELD()`	Parse Genbank file VERSION FIELD
Misc
`Bio2bstr()`	Convert sequence to Biostrings::*StringSet object
`bstr2BioString()`	Convert sequence to Biostrings::*StringSet object
`bstr_add_attr_for_object()`	Add object attribute
`bstr_add_attr_for_seq()`	Add sequence attribute
`class_bstr`	Common bstr class augments
`compare()`	Compare 2 residues
`mf()`	Calculate Oligo DNA Tm

Reference

bstr/dstr/astr class

S3 functions for bstr

functions for bstr

functions for dstr

Calculate

File IO

Misc

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