\textsc{Rime}: repeat identification

DOI10.1016/J.DAM.2013.02.016zbMATH Open1329.68312OpenAlexW2135938624MaRDI QIDQ496543FDOQ496543

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

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
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• scientific article; zbMATH DE number 1929946

zbMATH Keywords

\(q\)-gramsbiological sequencesmultiple alignmentrepetition finding

Mathematics Subject Classification ID

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

Cites Work

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

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

Uses Software

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

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