Cheatsheet

Every export, reached as bioseq.NAME. All errors are Error{kind: "bioinformatics"}.

jennifer

import "@deckyard/bioinformatics/" as bioseq;

Conventions (details): input in any case, residues out uppercase (FASTA/FASTQ parsing preserves case); offsets 0-based half-open, in forward-strand coordinates even for reverse-strand features; subrange is the one 1-based inclusive verb; filter* strip silently, everything else raises on a foreign character; physical quantities raise on ambiguity codes; a With suffix makes a default explicit.

Alphabets and validation

Function	Returns	Notes
`filterDna(s)`	`string`	keep `DNA_ALPHABET` only, uppercased
`filterRna(s)`	`string`	keep `RNA_ALPHABET` only
`filterProtein(s)`	`string`	keep `PROTEIN_ALPHABET` only
`isDna(s)`	`bool`	non-empty and wholly in the alphabet
`isRna(s)`	`bool`
`isProtein(s)`	`bool`
`kindName(kind)`	`string`	`"DNA"`, `"RNA"` or `"protein"`

Constant	Value	Meaning
`DNA`	`1`	molecule kind
`RNA`	`2`	molecule kind
`PROTEIN`	`3`	molecule kind
`DNA_ALPHABET`	`"ACGTRYSWKMBDHVN"`	bases plus IUPAC codes
`RNA_ALPHABET`	`"ACGURYSWKMBDHVN"`
`PROTEIN_ALPHABET`	`"ACDEFGHIKLMNPQRSTVWYBZXJUO*"`	standard, ambiguous, rare, stop

Transforms

Function	Returns	Notes
`complement(s)`	`string`	pairs each base, same order
`reverseComplement(s)`	`string`	the other strand, 5' to 3'
`reverse(s)`	`string`	any sequence
`transcribe(dna)`	`string`	T to U
`backTranscribe(rna)`	`string`	U to T
`translate(nt)`	`string`	standard code, stops as `*`
`translateWith(nt, table)`	`string`	codon map, e.g. `VERTEBRATE_MITOCHONDRIAL`
`translateFrame(nt, frame)`	`string`	frame 1, 2, 3, -1, -2, -3
`translateFrameWith(nt, frame, table)`	`string`
`sixFrame(nt)`	`list of Frame`	order 1, 2, 3, -1, -2, -3
`sixFrameWith(nt, table)`	`list of Frame`
`splitCodons(nt)`	`list of string`	trailing partial codon dropped
`oneToThree(protein)`	`string`	`MKV` to `MetLysVal`
`threeToOne(protein)`	`string`	run together or space/hyphen separated

`Frame`

Field	Meaning
`frame as int`	1, 2, 3, or -1, -2, -3 for the reverse complement
`protein as string`	the translation, stops as `*`

Composition and properties

Function	Returns	Notes
`baseCount(s)`	`map of string to int`	present residues only
`baseFrequency(s)`	`map of string to float`	percentages
`residueCount(p)`	`map of string to int`
`residueFrequency(p)`	`map of string to float`	percentages
`gcContent(s)`	`float`	percentage; ambiguity codes count in length only
`atContent(s)`	`float`	percentage of A, T, U
`gcWindows(s, size, step)`	`list of float`	full windows only
`molecularWeight(s, kind)`	`float`	average Da; nucleic acid as 5'-OH single strand
`meltingTemp(s)`	`float`	Wallace rule, Celsius, DNA
`meltingTempNn(s)`	`float`	nearest-neighbour, 250 nM primer, 50 mM Na+
`meltingTempNnWith(s, primerNm, saltMm)`	`float`	nM, mM
`netCharge(p, ph)`	`float`	EMBOSS `iep` pKa set
`isoelectricPoint(p)`	`float`	bisection over pH 0 to 14
`gravy(p)`	`float`	mean Kyte-Doolittle hydropathy
`aromaticity(p)`	`float`	fraction of F, W, Y
`dnaStats(s)`	`DnaStats`
`proteinStats(p)`	`ProteinStats`
`codonUsage(nt)`	`list of CodonUse`	standard code, first-seen order
`codonUsageWith(nt, table)`	`list of CodonUse`

`DnaStats`

Field	Meaning
`length as int`	bases
`gc as float`	GC percentage
`at as float`	AT percentage
`counts as map of string to int`	residue counts
`molecularWeight as float`	Da, 0.0 when ambiguous
`meltingTemp as float`	Wallace Tm, 0.0 when ambiguous
`ambiguous as bool`	any code other than A, C, G, T

`ProteinStats`

Field	Meaning
`length as int`	residues
`molecularWeight as float`	Da, 0.0 when ambiguous
`isoelectricPoint as float`	0.0 when ambiguous
`gravy as float`	0.0 when ambiguous
`aromaticity as float`	fraction of F, W, Y
`counts as map of string to int`	residue counts
`ambiguous as bool`	carries `B`, `Z`, `X`, `J` or `*`

`CodonUse`

Field	Meaning
`codon as string`	DNA-spelled codon
`aminoAcid as string`	its residue under the table, `X` if not in it
`count as int`	occurrences
`fraction as float`	share among synonymous codons, 0 to 1
`perThousand as float`	per thousand codons

Search

Function	Returns	Notes
`find(s, pattern)`	`list of Match`	exact, overlapping
`findIupac(s, pattern)`	`list of Match`	IUPAC codes in the pattern
`findFuzzy(s, pattern, maxMismatches)`	`list of Match`	substitutions only
`orfs(nt, minAa)`	`list of Orf`	six frames, standard code
`orfsWith(nt, minAa, tableId)`	`list of Orf`	NCBI table id
`cpgIslands(s, window, minGc, minObsExp)`	`list of Region`	classic: 200, 50.0, 0.6
`restrictionSites(s, names)`	`list of Site`	ordered by cut, then enzyme
`enzymesCutting(s)`	`list of string`	enzymes with a site
`nonCutters(s)`	`list of string`	enzymes without one
`restrictionDigest(s, names, circular)`	`list of Fragment`	cuts at `cutTop`

`Match`

Field	Meaning
`start as int`	0-based offset of the first base
`end as int`	one past the last base
`text as string`	the matched subsequence
`strand as int`	+1, or -1 on the reverse complement
`mismatches as int`	0 except for `findFuzzy`

`Orf`

Field	Meaning
`frame as int`	1, 2, 3 forward; -1, -2, -3 reverse
`strand as int`	sign of `frame`
`start as int`	first base of the start codon, forward coordinates
`end as int`	one past the last base, stop included
`length as int`	`end - start`
`nucleotides as string`	the frame as read, 5' to 3'
`protein as string`	translation without the stop
`stopped as bool`	false when it ran off the end

`Region`

Field	Meaning
`start as int`	0-based offset
`end as int`	one past the last base
`length as int`	bases
`gc as float`	GC percentage
`obsExp as float`	observed over expected CpG

`Site`

Field	Meaning
`enzyme as string`	enzyme name
`start as int`	first base of the recognition site
`end as int`	one past the site
`cut as int`	top-strand cut offset
`site as string`	concrete sequence found
`strand as int`	+1, or -1 if found only on the reverse strand

`Fragment`

Field	Meaning
`start as int`	first base in the original sequence
`end as int`	one past the last; not greater than `start` for a fragment through a circular origin
`length as int`	bases
`sequence as string`	the fragment

Formats

Function	Returns	Notes
`parseFasta(text)`	`list of Record`	case preserved
`writeFasta(records)`	`string`	wrapped at `FASTA_WIDTH`
`writeFastaWrapped(records, width)`	`string`
`wrap(s, width)`	`string`	no trailing newline
`toPlain(text)`	`string`	strip headers, digits, whitespace
`parseFastq(text)`	`list of Read`	four-line or wrapped
`writeFastq(reads)`	`string`	four-line form
`fastqToFasta(reads)`	`list of Record`
`qualityScores(r)`	`list of int`	Phred+33
`qualityScoresWith(r, offset)`	`list of int`	`PHRED33` or `PHRED64`
`meanQuality(r)`	`float`	arithmetic mean, Phred+33
`meanQualityWith(r, offset)`	`float`
`errorProbability(score)`	`float`	`10^(-Q/10)`

Constant	Value	Meaning
`FASTA_WIDTH`	`60`	default line width
`MAX_RECORDS`	`1000000`	records per parse
`PHRED33`	`33`	Sanger, Illumina 1.8+
`PHRED64`	`64`	Illumina 1.3 to 1.7

`Record`

Field	Meaning
`id as string`	first token after `>`
`description as string`	rest of the header, or ""
`sequence as string`	joined sequence lines

`Read`

Field	Meaning
`id as string`	first token after `@`
`description as string`	rest of the header, or ""
`sequence as string`	the bases
`quality as string`	encoded quality, same length as `sequence`

Manipulation

Function	Returns	Notes
`randomDna(n)`	`string`	uniform over `DNA_BASES`
`randomRna(n)`	`string`	uniform over `RNA_BASES`
`randomProtein(n)`	`string`	uniform over `STANDARD_RESIDUES`
`randomDnaWith(n, weights)`	`string`	relative weights
`randomRnaWith(n, weights)`	`string`
`randomProteinWith(n, weights)`	`string`
`shuffle(s)`	`string`	Fisher-Yates, composition kept
`mutate(s, rate, kind)`	`string`	substitutions, a mutated position always changes
`subrange(s, from, through)`	`string`	1-based inclusive
`windows(s, size, step)`	`list of string`	full windows only

Constant	Value	Meaning
`DNA_BASES`	`"ACGT"`	generator alphabet
`RNA_BASES`	`"ACGU"`
`STANDARD_RESIDUES`	`"ACDEFGHIKLMNPQRSTVWY"`

Comparison

Function	Returns	Notes
`alignGlobal(a, b, opts)`	`Alignment`	Needleman-Wunsch
`alignLocal(a, b, opts)`	`Alignment`	Smith-Waterman
`dnaOptions()`	`AlignOptions`	+2 / -1, gap -2
`proteinOptions()`	`AlignOptions`	`BLOSUM62`, gap -8
`substitutionScore(matrix, a, b)`	`int`	either pair order
`percentIdentity(al)`	`float`	over alignment length
`percentSimilarity(al)`	`float`
`percentGaps(al)`	`float`
`formatAlignment(al, width)`	`string`	EMBOSS-style blocks
`hammingDistance(a, b)`	`int`	equal lengths only
`editDistance(a, b)`	`int`	Levenshtein

Constant	Value	Meaning
`DEFAULT_MAX_ALIGNMENT_CELLS`	`1000000`	default `maxCells`, about 1 GB

`AlignOptions`

Field	Meaning
`matchScore as int`	identical residues, when `matrix` is empty
`mismatchScore as int`	differing residues, when `matrix` is empty
`gapScore as int`	per gap position
`matrix as map of string to int`	substitution matrix, or empty
`maxCells as int`	DP matrix limit; 0 for none

`Alignment`

Field	Meaning
`a as string`	first sequence, gapped
`b as string`	second sequence, gapped
`markup as string`	`\|` identical, `:` similar, space otherwise
`score as int`	total score
`length as int`	columns
`identities as int`	identical columns
`similarities as int`	positively scoring columns, identities included
`gaps as int`	gap columns
`startA as int`	0-based start in the first sequence
`startB as int`	0-based start in the second

Reference data

Function	Returns	Notes
`codonTable(id)`	`map of string to string`	NCBI `transl_table`
`codonTableName(id)`	`string`
`codonTableIds()`	`list of int`	1-6, 9-11
`startCodons(id)`	`list of string`
`expandIupac(code)`	`string`	`R` to `AG`
`iupacClass(code)`	`string`	`R` to `[AG]`
`matchesIupac(code, base)`	`bool`	one-way
`aminoAcid(code)`	`AminoAcid`	one- or three-letter code
`aminoAcids()`	`list of AminoAcid`	22 records
`hasAminoAcid(code)`	`bool`
`enzyme(name)`	`Enzyme`	case-insensitive
`hasEnzyme(name)`	`bool`
`enzymes()`	`list of Enzyme`	alphabetical
`enzymeNames()`	`list of string`	alphabetical
`isoschizomers(name)`	`list of string`	same site string
`isBlunt(e)`	`bool`	`cutTop == cutBottom`

Constant	Value	Meaning
`PKA_N_TERMINUS`	`8.6`	EMBOSS `iep`
`PKA_C_TERMINUS`	`3.6`	EMBOSS `iep`
`WATER_MONO_MASS`	`18.010565`	Da
`WATER_AVG_MASS`	`18.01528`	Da
`PHOSPHATE_MASS`	`79.98`	Da, HPO3
`GAS_CONSTANT`	`1.987`	cal/(mol K)

Map constants:

Constant	Type	Value
`STANDARD`	`map of string to string`	NCBI code 1
`VERTEBRATE_MITOCHONDRIAL`	`map of string to string`	code 2
`YEAST_MITOCHONDRIAL`	`map of string to string`	code 3
`MOLD_MITOCHONDRIAL`	`map of string to string`	code 4
`INVERTEBRATE_MITOCHONDRIAL`	`map of string to string`	code 5
`CILIATE_NUCLEAR`	`map of string to string`	code 6
`ECHINODERM_MITOCHONDRIAL`	`map of string to string`	code 9
`EUPLOTID_NUCLEAR`	`map of string to string`	code 10
`BACTERIAL`	`map of string to string`	code 11
`IUPAC_DNA`	`map of string to string`	code to bases
`IUPAC_RNA`	`map of string to string`	code to bases
`COMPLEMENT_DNA`	`map of string to string`	code to complement
`COMPLEMENT_RNA`	`map of string to string`	code to complement
`THREE_LETTER`	`map of string to string`	one-letter to three-letter
`DNA_RESIDUE_MASS`	`map of string to float`	average residue mass, Da
`RNA_RESIDUE_MASS`	`map of string to float`	average residue mass, Da
`NN_ENTHALPY`	`map of string to float`	dinucleotide dH, kcal/mol
`NN_ENTROPY`	`map of string to float`	dinucleotide dS, cal/(mol K)
`BLOSUM62`	`map of string to int`	pair to score, one order per pair

`AminoAcid`

Field	Meaning
`one as string`	one-letter code
`three as string`	three-letter code
`name as string`	full name
`monoMass as float`	monoisotopic residue mass, Da
`avgMass as float`	average residue mass, Da
`pKa as float`	side chain, 0.0 if it does not ionise
`charge as int`	+1, -1 or 0
`hydropathy as float`	Kyte-Doolittle

`Enzyme`

Field	Meaning
`name as string`	conventional spelling
`site as string`	recognition sequence, IUPAC
`cutTop as int`	top-strand cut offset into the site
`cutBottom as int`	bottom-strand cut, counted along the top strand
`overhang as string`	`"5'"`, `"3'"` or `"blunt"`
`overhangLength as int`	0 when blunt

#Cheatsheet

#Alphabets and validation

#Transforms

#Frame

#Composition and properties

#DnaStats

#ProteinStats

#CodonUse

#Search

#Match

#Orf

#Region

#Site

#Fragment

#Formats

#Record

#Read

#Manipulation

#Comparison

#AlignOptions

#Alignment

#Reference data

#AminoAcid

#Enzyme