Linear time minimum segmentation enables scalable founder reconstruction

Autor: Tuukka Norri, Bastien Cazaux, Dmitry Kosolobov, Veli Mäkinen

Publikováno v: Algorithms for Molecular Biology, Vol 14, Iss 1, Pp 1-15 (2019)

Abstract Background We study a preprocessing routine relevant in pan-genomic analyses: consider a set of aligned haplotype sequences of complete human chromosomes. Due to the enormous size of such data, one would like to represent this input set with

Externí odkaz: https://doaj.org/article/f184131ea832445884b76629a936afa6

Linear Time Maximum Segmentation Problems in Column Stream Model

Autor: Veli Mäkinen, Bastien Cazaux, Dmitry Kosolobov, Tuukka Norri

Publikováno v: Lect. Notes Comput. Sci.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
String Processing and Information Retrieval ISBN: 9783030326852
SPIRE

We study a lossy compression scheme linked to the biological problem of founder reconstruction: The goal in founder reconstruction is to replace a set of strings with a smaller set of founders such that the original connections are maintained as well

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::163a803d2a668262a5216db5cff80e47
https://helda.helsinki.fi/bitstream/10138/322257/1/fragment_spire_final.pdf

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Towards pan-genome read alignment to improve variation calling.

Autor: Valenzuela, Daniel¹, Norri, Tuukka¹, Välimäki, Niko², Pitkänen, Esa³, Mäkinen, Veli¹ veli.makinen@helsinki.fi

Publikováno v: BMC Genomics. 5/9/2018 Supplement 2, Vol. 19, p123-130. 8p. 2 Diagrams, 2 Charts.

seq-seq-pan: building a computational pan-genome data structure on whole genome alignment.

Autor: Jandrasits, Christine¹ JandrasitsC@rki.de, Dabrowski, Piotr W.¹ DabrowskiW@rki.de, Fuchs, Stephan² FuchS@rki.de, Renard, Bernhard Y.¹ RenardB@rki.de

Publikováno v: BMC Genomics. 1/15/2018, Vol. 19, p1-N.PAG. 12p. 2 Diagrams, 6 Charts, 1 Graph.