![]() Otherwise, they must contain sequences that are the same.įindPalindromes returns an XStringViews object containing all Must contain sequences that are reverse complement from each other. If the subject string is a nucleotide sequence (i.e. palindromes where the 2 arms are separated by an arbitrary Palindromes or 2-arm palindromes (the former being a particular case of The palindromes that can be searched for are either strict The findPalindromes function finds palindromic substrings in a subject XStringViews object containing a set of 2-arm palindromes. The maximum number of mismatching letters allowed between the 2 arms ofĪn XString object containing a 2-arm palindrome, or an Note that by default ( max.looplength=1), findPalindromesĪn integer giving the minimum length of "the loop" of the palindromes Separating the 2 arms) of the palindromes to search for. stringDist: String Distance/Alignment Score MatrixįindPalindromes ( subject, min.armlength = 4, max.looplength = 1, min.looplength = 0, max.mismatch = 0 ) palindromeArmLength ( x, max.mismatch = 0 ) palindromeLeftArm ( x, max.mismatch = 0 ) palindromeRightArm ( x, max.mismatch = 0 )Īn XString object containing the subject string,Īn integer giving the minimum length of the arms of the palindromesĪn integer giving the maximum length of "the loop" (i.e the sequence.reverseComplement: Sequence reversing and complementing.replaceLetterAt: Replacing letters in a sequence (or set of sequences) at some.replaceAt: Extract/replace arbitrary substrings from/in a string or set.QualityScaledXStringSet-class: QualityScaledBStringSet, QualityScaledDNAStringSet.pmatchPattern: Longest Common Prefix/Suffix/Substring searching functions.phiX174Phage: Versions of bacteriophage phiX174 complete genome and sample.PairwiseAlignments-io: Write a PairwiseAlignments object to a file.PairwiseAlignments-class: PairwiseAlignments, PairwiseAlignmentsSingleSubject, and.pairwiseAlignment: Optimal Pairwise Alignment.nucleotideFrequency: Calculate the frequency of oligonucleotides in a DNA or RNA.needwunsQS: (Deprecated) Needleman-Wunsch Global Alignment.MultipleAlignment-class: MultipleAlignment objects.match-utils: Utility functions operating on the matches returned by a.matchPWM: PWM creating, matching, and related utilities.matchprobes: A function to match a query sequence to the sequences of a.matchProbePair: Find "theoretical amplicons" mapped to a probe pair.matchPDict-inexact: Inexact matching with matchPDict()/countPDict()/whichPDict().matchPDict-exact: Matching a dictionary of patterns against a reference.matchPattern: String searching functions.matchLRPatterns: Find paired matches in a sequence.maskMotif: Masking by content (or by position).MaskedXString-class: MaskedXString objects.lowlevel-matching: Low-level matching functions.longestConsecutive: Obtain the length of the longest substring containing only.letterFrequency: Calculate the frequency of letters in a biological sequence.IUPAC_CODE_MAP: The IUPAC Extended Genetic Alphabet.injectHardMask: Injecting a hard mask in a sequence.HNF4alpha: Known HNF4alpha binding sequences.gregexpr2: A replacement for R standard gregexpr function.GENETIC_CODE: The Standard Genetic Code and its known variants.findPalindromes: Searching a sequence for palindromes.dinucleotideFrequencyTest: Pearson's chi-squared Test and G-tests for String Position.detail: Show (display) detailed object content.chartr: Replace letters in a sequence or set of sequences.Biostrings-internals: Biostrings internals. ![]() AMINO_ACID_CODE: The Single-Letter Amino Acid Code.align-utils: Utility functions related to sequence alignment.AlignedXStringSet-class: AlignedXStringSet and QualityAlignedXStringSet objects.
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