SIS: a program to generate draft genome sequence scaffolds for prokaryotes.

BMC Bioinformatics
Zanoni DiasJoão C Setubal

Abstract

Decreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome comparisons and guide gap closure efforts. One popular technique for obtaining contig scaffolds is to map contigs onto a reference genome. However, rearrangements that may exist between the query and reference genomes may result in incorrect scaffolds, if these rearrangements are not taken into account. Large-scale inversions are common rearrangement events in prokaryotic genomes. Even in draft genomes it is possible to detect the presence of inversions given sufficient sequencing coverage and a sufficiently close reference genome. We present a linear-time algorithm that can generate a set of contig scaffolds for a draft genome sequence represented in contigs given a reference genome. The algorithm is aimed at prokaryotic genomes and relies on the presence of matching sequence patterns between the query and reference genomes that can be interpreted as the result of large-scale inversions; we call these patterns inversion signatures. Our algorithm is capable of correctly generating a scaffold if at least one member of every inversio...Continue Reading

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Citations

Jun 14, 2013·BMC Bioinformatics·Chi-Long LiChin Lung Lu
Jan 30, 2014·PloS One·Vasundhara PaliwalHemant J Purohit
Nov 29, 2014·BMC Bioinformatics·Chin Lung LuHsien-Tai Chiu
Aug 8, 2015·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Chin Lung Lu
Dec 12, 2018·Microbiology Resource Announcements·Steven A HigginsFrank E Löffler
Feb 6, 2017·BMC Bioinformatics·Kun-Tze ChenChin Lung Lu
Sep 13, 2017·Genetics and Molecular Biology·Frederico Schmitt KremerLuciano da Silva Pinto
Jan 2, 2019·BMC Systems Biology·Kun-Tze ChenChin Lung Lu
Feb 27, 2021·Briefings in Bioinformatics·Junwei LuoChaokun Yan
Aug 28, 2020·Systematic and Applied Microbiology·Caroline LeyerVincent Cattoir

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Software Mentioned

PGA4genomics
nucmer
Primer3
r2cat
BLAT
CONTIGuator
promer
Projector
Mauve
GRIL

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