There are many tools developed to compute the counts of k-mers present in a gene sequence. Jellyfish, Bloom Filter Counter, DSK Kmer Counter, KAnalyze, KMC 2 etc are some efficient software developed in last decade to count k-mers.

But in what purpose, these tools are used?

How they are serving biological community?

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    $\begingroup$ What we have used this approach for is to search for k-mers that are enriched, or over-represented, in one genomic interval (or intervals), while present at the expected, or anticipated, frequency in the rest of the genome. The hypothesis being that such k-mers may have a biological role, either in gene regulation, or chromosome structure and function. With a collection of these k-mers in hand, one can attempt to test the hypothesis. For example, if you had a list of human neuronal enhancers, you could ask if there are any enriched k-mers, etc. $\endgroup$ – mdperry Apr 10 '16 at 18:07
  • $\begingroup$ @mdperry Can I also use what you said to detect repeat elements like copy-number variation? $\endgroup$ – SmallChess Apr 18 '16 at 12:36
  • $\begingroup$ I have not seen an application like that; but one could try. It seems to me that if you had two genomes, Normal, and Mutant, you could run the k-mer counts and compare them, to pick up repeated k-mers. However most of the CNV approaches I have seen in the literature have used micro arrays OR deep sequencing read depths. $\endgroup$ – mdperry Apr 18 '16 at 17:24

The applications for counting the k-mer occurences in a sequence are: building de Bruijn graphs [1] for de novo assembly from very large number of short reads, produced by next generation sequencing, fast multiple sequence alignment [2], and [3] repeat detection.

  1. Compeau PE, Pevzner PA, Tesler G: How to apply de Bruijn graphs to genome assembly. Nature Biotechnol. 2011, 29 (11): 987-991. 10.1038/nbt.2023

  2. Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32 (5): 1792-1797. 10.1093/nar/gkh340

  3. Kurtz S, Narechania A, Stein J, Ware D: A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics. 2008, 9 (1): 517-10.1186/1471-2164-9-517

To be clear, here is the biological significance of each of these applications:

  1. Sequencing any genomes (bacterial, plant, mammalian) has become very cheap and easy recently with the next generation sequencing technologies. As opposed to the Sanger sequencing (the first generation), these produce as a readout very short sequencing reads, which have to be assembled into longer ones, and subsequently, into whole genomes. Counting the k-mers is part of the assembly process and this is its biological importance.

  2. In order to compare whether proteins might have similar function, and thus belong to the same protein family, a multiple sequence alignment is performed. This is crucial step when annotating new protein sequences and studying their biological functions.

  3. There are many repeats in our genome, as well as in plants. Repeated sequences are also involved in neurodegenerative diseases such as Hungtingtons, so being able to identify them is of medicinal importance.

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  • $\begingroup$ At first thank you for trying to answer me, but all these three things are known to me, because those are described in almost all papers of the tools I have mentioned like kmc2, jellyfish etc. It still not biological to me. I am seeking the last effect on biology. Say, on your answer, the question comes in mind is What is the biological significance of de Bruijn graphs, ast multiple sequence alignment and repeat detection? Thanks again. $\endgroup$ – Enamul Hassan Apr 8 '16 at 3:30
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    $\begingroup$ These 3 applications are fundamental in biology. I gave short descriptions of each one. You can look them up if you want to know more. $\endgroup$ – Gergana Vandova Apr 8 '16 at 5:29
  • $\begingroup$ @manetsus That should be asked in a different question. Plus, a question like "what is the importance of de Bruijn graphs in biology" is quite broad. You can have a look at Pavel Pevzner's review on how Eulerian path is used for genome assembly and ask a specific question. $\endgroup$ – WYSIWYG Apr 8 '16 at 7:39

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