\textsc{Rime}: repeat identification

DOI10.1016/J.DAM.2013.02.016MaRDI QIDQ496543zbMATH OpenOpenAlexFDO

Authors Maria Federico, Pierre Peterlongo, Nadia Pisanti, Marie-France Sagot

Publication date 22 September 2015

Published in Discrete Applied Mathematics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.dam.2013.02.016

zbMATH Keywords

\(q\)-gramsbiological sequencesmultiple alignmentrepetition finding

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Algorithms on strings (68W32)

Recommendations

• Fast algorithm for Vernier search of long repeats in DNA sequences with bounded error density
• Lossless filter for multiple repetitions with Hamming distance
• A linear algorithm for the detection of evolutive tandem repeats
• Alphabet-independent algorithms for finding context-sensitive repeats in linear time
• scientific article; zbMATH DE number 1929946

Cites work

• A FIRST APPROACH TO FINDING COMMON MOTIFS WITH GAPS
• Algorithm 457: finding all cliques of an undirected graph
• Enumerating all connected maximal common subgraphs in two graphs
• Extracting string motif bases for quorum higher than two
• Lossless filter for multiple repetitions with Hamming distance

Cited in

(3)

• Fast algorithm for Vernier search of long repeats in DNA sequences with bounded error density
• Motif trie: an efficient text index for pattern discovery with don't cares
• Lossless filter for multiple repetitions with Hamming distance

Describes a project that uses

Uses Software

• MADMX
• Algorithm 457
• LTR_FINDER
• T-coffee
• Kalign
• MUSCLE
• LAGAN
• Varun
• Repseek
• DIALIGN-TX
• ClustalW
• DIALIGN

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