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Items: 1 to 20 of 207


Short read sequence typing (SRST): multi-locus sequence types from short reads.

Inouye M, Conway TC, Zobel J, Holt KE.

BMC Genomics. 2012 Jul 24;13:338.


Multilocus sequence typing of total-genome-sequenced bacteria.

Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O.

J Clin Microbiol. 2012 Apr;50(4):1355-61. doi: 10.1128/JCM.06094-11. Epub 2012 Jan 11.


MLSTest: novel software for multi-locus sequence data analysis in eukaryotic organisms.

Tomasini N, Lauthier JJ, Llewellyn MS, Diosque P.

Infect Genet Evol. 2013 Dec;20:188-96. doi: 10.1016/j.meegid.2013.08.029. Epub 2013 Sep 8.


Bayesian semi-supervised classification of bacterial samples using MLST databases.

Cheng L, Connor TR, Aanensen DM, Spratt BG, Corander J.

BMC Bioinformatics. 2011 Jul 26;12:302. doi: 10.1186/1471-2105-12-302.


The multilocus sequence typing network:

Aanensen DM, Spratt BG.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W728-33.


Optimization of Bartonella henselae multilocus sequence typing scheme using single-nucleotide polymorphism analysis of SOLiD sequence data.

Zhao F, Chaloner G, Darby A, Song XP, Li DM, Birtles R, Liu QY.

Chin Med J (Engl). 2012 Jul;125(13):2284-8.


A curated public database for multilocus sequence typing (MLST) and analysis of Haemophilus parasuis based on an optimized typing scheme.

Mullins MA, Register KB, Brunelle BW, Aragon V, Galofré-Mila N, Bayles DO, Jolley KA.

Vet Microbiol. 2013 Mar 23;162(2-4):899-906. doi: 10.1016/j.vetmic.2012.11.019. Epub 2012 Nov 20.


SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.

Pattnaik S, Gupta S, Rao AA, Panda B.

BMC Bioinformatics. 2014 Feb 5;15:40. doi: 10.1186/1471-2105-15-40.


BIGSdb: Scalable analysis of bacterial genome variation at the population level.

Jolley KA, Maiden MC.

BMC Bioinformatics. 2010 Dec 10;11:595. doi: 10.1186/1471-2105-11-595.


Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach.

Francisco AP, Bugalho M, Ramirez M, Carriço JA.

BMC Bioinformatics. 2009 May 18;10:152. doi: 10.1186/1471-2105-10-152.


Sequence analysis of 96 genomic regions identifies distinct evolutionary lineages within CC156, the largest Streptococcus pneumoniae clonal complex in the MLST database.

Moschioni M, Lo Sapio M, Crisafulli G, Torricelli G, Guidotti S, Muzzi A, Barocchi MA, Donati C.

PLoS One. 2013 Apr 12;8(4):e61003. doi: 10.1371/journal.pone.0061003. Print 2013.


PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods.

Francisco AP, Vaz C, Monteiro PT, Melo-Cristino J, Ramirez M, Carriço JA.

BMC Bioinformatics. 2012 May 8;13:87. doi: 10.1186/1471-2105-13-87.


mlstdbNet - distributed multi-locus sequence typing (MLST) databases.

Jolley KA, Chan MS, Maiden MC.

BMC Bioinformatics. 2004 Jul 1;5:86.


Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions.

Laing C, Buchanan C, Taboada EN, Zhang Y, Kropinski A, Villegas A, Thomas JE, Gannon VP.

BMC Bioinformatics. 2010 Sep 15;11:461. doi: 10.1186/1471-2105-11-461.


The utility of high-resolution melting analysis of SNP nucleated PCR amplicons--an MLST based Staphylococcus aureus typing scheme.

Lilliebridge RA, Tong SY, Giffard PM, Holt DC.

PLoS One. 2011;6(6):e19749. doi: 10.1371/journal.pone.0019749. Epub 2011 Jun 22.


Fast and accurate short read alignment with Burrows-Wheeler transform.

Li H, Durbin R.

Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18.


Software for selecting the most informative sets of genomic loci for multi-target microbial typing.

O'Sullivan MV, Sintchenko V, Gilbert GL.

BMC Bioinformatics. 2013 May 1;14:148. doi: 10.1186/1471-2105-14-148.


Ψ-RA: a parallel sparse index for genomic read alignment.

Oğuzhan Külekci M, Hon WK, Shah R, Scott Vitter J, Xu B.

BMC Genomics. 2011;12 Suppl 2:S7. doi: 10.1186/1471-2164-12-S2-S7. Epub 2011 Jul 27.


Allele intersection analysis: a novel tool for multi locus sequence assignment in multiply infected hosts.

Arthofer W, Riegler M, Schuler H, Schneider D, Moder K, Miller WJ, Stauffer C.

PLoS One. 2011;6(7):e22198. doi: 10.1371/journal.pone.0022198. Epub 2011 Jul 15.


Meningococcus genome informatics platform: a system for analyzing multilocus sequence typing data.

Katz LS, Bolen CR, Harcourt BH, Schmink S, Wang X, Kislyuk A, Taylor RT, Mayer LW, Jordan IK.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W606-11. doi: 10.1093/nar/gkp288. Epub 2009 May 25.

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