Contents
What is k-mer counting?
k-mer counting involves counting the number of substrings that have length k in a string S, or a set of strings, where k is a positive integer. Let ∑ = {A, C, G, T, N} denote the alphabet of DNA nucleotide sequences, where N denotes an undetermined character.
What is k-mer composition?
Usually, the term k-mer refers to all of a sequence’s subsequences of length , such that the sequence AGAT would have four monomers (A, G, A, and T), three 2-mers (AG, GA, AT), two 3-mers (AGA and GAT) and one 4-mer (AGAT). More generally, a sequence of length will have k-mers and total possible k-mers, where.
What are Canonical Kmers?
When counting canonical kmers, ie kmers in which both the forward and reverse complement of a sequence are treated as identical, how do kmer counting programs decide which kmer to use as the canonical sequence? So, it looks like KMCs’ ‘canonical’ kmers are the ones that first occur alphabetically.
What is a K-Mer and why is it so influential in transcriptome assembly?
A contig is assembled by following the connected nodes and edges through the graph. Thus, the length of the chosen k-mer influences the connectivity between the nodes and can affect the result of the assembly considerably.
What is Mer in genetics?
Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. The length of the oligonucleotide is usually denoted by “-mer” (from Greek meros, “part”).
What is the reverse complement?
Reverse Complement. Reverse Complement converts a DNA sequence into its reverse, complement, or reverse-complement counterpart. The entire IUPAC DNA alphabet is supported, and the case of each input sequence character is maintained.
What are the different types of k-mer counting?
K-mer counting is not one of those labyrinthine problems which are complicated and confusing. It is a very simple problem where you count the frequency of each k-mer in the given sequence. We usually look for three different types of frequencies: total count, distinct count, and unique count. Let’s consider the aforementioned DNA sequence again.
How to count kmers with a MER key?
For a more complex use case, you can provide a four-column BED file with the interval’s genomic sequence in the fourth column ( i.e., ID field), along with the number k for the k-mers you want to count, an offset value for mer-keys (explained below), and a results directory to write results, e.g.:
How are distinct k-mers counted in bioinformatics?
The distinct k-mers are counted only once regardless of how many times they appear. For example, even though ACGA has appeared twice, we count it only once. The Distinct Count provides us the information of whether a k-mer has appeared or not (not how many times it has appeared). The unique k-mers are those which appear only once.
What is the Khmer library for k mer counting?
khmer ktables are a simple C++ library for counting k-mers in DNA sequences. There’s a complete Python wrapping and it should be pretty darned fast; it’s intended for genome-scale k-mer counting. ‘ktable’s are a table of 4**k counters. khmer then maps each k-mer into this table with a simple (and reversible) hash function.