![]() ![]() 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. ![]() The CRISPR and spacer sequences are followed by a region for an RNA molecule known as tracrRNA, which guides the cutting molecules and the crRNA to their target locations on the virus DNA. These genes provide the blueprint for the Cas proteins - namely, the enzymes that cut the DNA strand. Other genes known as CRISPR-associated genes (Cas) are located adjacent to it. The CRISPR region includes a promoter which ensures that the CRISPR region can be read and translated into the CRISPR-RNA (crRNA). They originated from the genome of foreign DNA that penetrated the bacterial cell, and are also known as spacer DNA. Variable regions of similar length can be found between these sequences. ![]() They range between 23 and 47 base pairs in length. Out of the palindromic sequences of the CRISPR region RNA molecules are transcribed, which adopt a very stable arrangement (secondary structure). These sequences can be four, six or eight base pairs long, although some cutting proteins require 20 or more base pairs. DNA-cutting proteins frequently use palindrome sequences as recognition sequences, at which they cut the DNA molecule. Nevertheless, they are not entirely meaningless. Unlike word palindromes like ‘civic’ and ‘tenet’, which have a meaning, the palindromes in the genetics dictionary do not make sense and cannot be translated into functional proteins. This is the property that gives CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) its tongue-twisting name. In these sequences, the letters of the genetic code, the four base molecules adenine, cytosine, thymine and guanine, are ordered such that they have the same order as the second complementary DNA-strand – in this case read in opposite direction. The beginning of the CRISPR revolution was marked by the discovery of a large number of repeated palindromic sequences in a region of bacterial DNA. “Able was I ere I saw Elba”: this rather bombastic statement is a palindrome sentence, in other words it reads exactly the same forwards as it does backwards. ![]()
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