Alignment-Free Sequence Analysis and Applications
نویسندگان
چکیده
منابع مشابه
Alignment-Free Sequence Analysis and Applications
Genome and metagenome comparisons based on large amounts of next generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads. Alignment-free approaches based on the counts of word patterns in NGS data do not depend on the complete genome and are generally computationally efficient. Thus, they ...
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Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software,...
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With the massive production of genomic and proteomic data, the number of available biological sequences in databases has reached a level that is not feasible anymore for exact alignments even when just a fraction of all sequences is used. To overcome this inevitable time complexity, ultrafast alignment-free methods are studied. Within the past two decades, a broad variety of nonalignment method...
متن کاملMultiple alignment-free sequence comparison
MOTIVATION Recently, a range of new statistics have become available for the alignment-free comparison of two sequences based on k-tuple word content. Here, we extend these statistics to the simultaneous comparison of more than two sequences. Our suite of statistics contains, first, C(*)1 and C(S)1, extensions of statistics for pairwise comparison of the joint k-tuple content of all the sequenc...
متن کاملAlignment-free Sequence Analysis Using Extensible Markov Models
Profile models based on Hidden Markov Models (HMM) for sequence studies have gained visibility among researchers. While the mathematical foundation, the proven algorithms such as Viterbi, Forward and Backward algorithms have certainly provided a rigorous probabilistic platform, the requirement of classic alignment has ensured an extremely high time complexity. We propose the use of another kind...
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ژورنال
عنوان ژورنال: Annual Review of Biomedical Data Science
سال: 2018
ISSN: 2574-3414,2574-3414
DOI: 10.1146/annurev-biodatasci-080917-013431