Repseek, a tool to retrieve approximate repeats from large DNA sequences
نویسندگان
چکیده
منابع مشابه
Repseek, a tool to retrieve approximate from large DNA sequences
The importance of genome redundancy has been strongly emphasized in the field of genome dynamics and evolution as well as in medical biology. A repeat is a sequence present twice or more with a high degree of similarity within a larger sequence (e.g. a chromosome) or set of sequences (e.g. a genome with several chromosomes). Each instance of the repeated sub-sequence is called a ’copy’ of the r...
متن کاملRepseek, a tool to retrieve approximate repeats from large DNA sequences
UNLABELLED Chromosomes or other long DNA sequences contain many highly similar repeated sub-sequences. While there are efficient methods for detecting strict repeats or detecting already characterized repeats, there is no software available for detecting approximate repeats in large DNA sequences allowing for weighted substitutions and indels in a coherent statistical framework. Here, we presen...
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We study the problem of finding supermaximal repeats in large DNA sequences. For this, we propose an algorithm called SMR which uses an auxiliary index structure (POL), which is derived from and replaces the suffix tree index STTD64 [1]. The results of our numerous experiments using the 24 human chromosomes data indicate that SMR outperforms the solution provided as part of the Vmatch [2] softw...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2006
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btl519