SABmark

SABmark - a benchmark for sequence alignment that covers the entire known fold space. Summary: The Sequence Alignment Benchmark (SABmark) provides sets of multiple alignment problems derived from the SCOP classification. These sets, Twilight Zone and Superfamilies, both cover the entire known fold space using sequences with very low to low, and low to intermediate similarity, respectively. In addition, each set has an alternate version in which unalignable but apparently similar sequences are added to each problem. Availability: SABmark is available from http://bioinformatics.vub.ac.be


References in zbMATH (referenced in 9 articles )

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  1. DeBlasio, Dan; Kececioglu, John: Parameter advising for multiple sequence alignment (2017)
  2. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  3. Nguyen, Ken; Guo, Xuan; Pan, Yi: Multiple biological sequence alignment. Scoring functions, algorithms and evaluation (2016)
  4. Warnow, Tandy: Large-scale multiple sequence alignment and phylogeny estimation (2013)
  5. Hara, Toshihide; Sato, Keiko; Ohya, Masanori: MTRAP: pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues (2010) ioport
  6. Kim, Jaebum; Sinha, Saurabh: Towards realistic benchmarks for multiple alignments of non-coding sequences (2010) ioport
  7. Jiang, Haiyan; Blouin, Christian: Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions (2007) ioport
  8. Kim, Changhoon; Lee, Byungkook: Accuracy of structure-based sequence alignment of automatic methods (2007) ioport
  9. Won, Kyoung-Jae; Hamelryck, Thomas; PrĂ¼gel-Bennett, Adam; Krogh, Anders: An evolutionary method for learning HMM structure: Prediction of protein secondary structure (2007) ioport