\textsc{Rime}: repeat identification

DOI10.1016/j.dam.2013.02.016zbMath1329.68312OpenAlexW2135938624MaRDI QIDQ496543

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

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

biological sequencesmultiple alignment\(q\)-gramsrepetition finding

Mathematics Subject Classification ID

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

Related Items

Motif trie: an efficient text index for pattern discovery with don't cares

Uses Software

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

Cites Work

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