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LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search.
Will S, Siebauer MF, Heyne S, Engelhardt J, Stadler PF, Reiche, Backofen R. Will S, et al. Algorithms Mol Biol. 2013 Apr 20;8:14. doi: 10.1186/1748-7188-8-14. eCollection 2013. Algorithms Mol Biol. 2013. PMID: 23601347 Free PMC article.
As a search engine we devised a semi-global scanning variant of LocARNA's algorithm for sequence-structure alignment. The LocARNAscan tool is optimized for speed and low memory consumption. ...In transcriptome-wide applications, such methods will provide accurate st …
As a search engine we devised a semi-global scanning variant of LocARNA's algorithm for sequence-structure alignment. The LocARNAscan …
Bi-alignments with affine gaps costs.
Stadler PF, Will S. Stadler PF, et al. Among authors: will s. Algorithms Mol Biol. 2022 May 16;17(1):10. doi: 10.1186/s13015-022-00219-7. Algorithms Mol Biol. 2022. PMID: 35578255 Free PMC article.
AVAILABILITY: The affine cost bi-alignment algorithm has been implemented in Python 3 and Cython. It is available as free software from https://github.com/s-will/BiAlign/releases/tag/v0.3 and as bioconda package bialign....
AVAILABILITY: The affine cost bi-alignment algorithm has been implemented in Python 3 and Cython. It is available as free software from http …
Local sequence-structure motifs in RNA.
Backofen R, Will S. Backofen R, et al. Among authors: will s. J Bioinform Comput Biol. 2004 Dec;2(4):681-98. doi: 10.1142/s0219720004000818. J Bioinform Comput Biol. 2004. PMID: 15617161
Lifting prediction to alignment of RNA pseudoknots.
Möhl M, Will S, Backofen R. Möhl M, et al. Among authors: will s. J Comput Biol. 2010 Mar;17(3):429-42. doi: 10.1089/cmb.2009.0168. J Comput Biol. 2010. PMID: 20377455
Recent advances in RNA folding.
Fallmann J, Will S, Engelhardt J, Grüning B, Backofen R, Stadler PF. Fallmann J, et al. Among authors: will s. J Biotechnol. 2017 Nov 10;261:97-104. doi: 10.1016/j.jbiotec.2017.07.007. Epub 2017 Jul 8. J Biotechnol. 2017. PMID: 28690134 Free article. Review.
216 results