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The Burrows–Wheeler transform (BWT, also called block-sorting compression) rearranges a character string into runs of similar characters. This is useful for compression, since it tends to be easy to compress a string that has runs of repeated characters by techniques such as move-to-front transform and run-length encoding.
String 1 admits a short linguistic description: "32 repetitions of '01'". This description has 22 characters, and it can be efficiently constructed out of some basis sequences. [ clarification needed ] String 2 has no obvious simple description other than writing down the string itself, which has 64 characters, [ clarification needed ] and it ...
In this example, we will consider a dictionary consisting of the following words: {a, ab, bab, bc, bca, c, caa}. The graph below is the Aho–Corasick data structure constructed from the specified dictionary, with each row in the table representing a node in the trie, with the column path indicating the (unique) sequence of characters from the root to the node.
Used in Python 2.3 and up, and Java SE 7. Insertion sorts Insertion sort: determine where the current item belongs in the list of sorted ones, and insert it there; Library sort; Patience sorting; Shell sort: an attempt to improve insertion sort; Tree sort (binary tree sort): build binary tree, then traverse it to create sorted list
procedure k-mers(string seq, integer k) is L ← length(seq) arr ← new array of L − k + 1 empty strings // iterate over the number of k-mers in seq, // storing the nth k-mer in the output array for n ← 0 to L − k + 1 exclusive do arr[n] ← subsequence of seq from letter n inclusive to letter n + k exclusive return arr
fastqp Simple FASTQ quality assessment using Python. Kraken: [9] A set of tools for quality control and analysis of high-throughput sequence data. HTSeq [10] The Python script htseq-qa takes a file with sequencing reads (either raw or aligned reads) and produces a PDF file with useful plots to assess the technical quality of a run.
An xorshift* generator applies an invertible multiplication (modulo the word size) as a non-linear transformation to the output of an xorshift generator, as suggested by Marsaglia. [1] All xorshift* generators emit a sequence of values that is equidistributed in the maximum possible dimension (except that they will never output zero for 16 ...
For one-dimensional arrays, this facility may be provided as an operation append(A,x) that increases the size of the array A by one and then sets the value of the last element to x. Other array types (such as Pascal strings) provide a concatenation operator, which can be used together with slicing to achieve that effect and more.