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Sequence analysis (applications) Section edited by Mihai Pop

This section incorporates all aspects of sequence analysis applications, including but not limited to: software, workflows and webservers dealing with applied sequence/genome analysis, sequence assembly, analysis of sequence features, and protein function and ligand binding, estimated through sequence features.

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1.

Methodology article   Open Access

Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data

Thorfinn Sand Korneliussen, Ida Moltke, Anders Albrechtsen, Rasmus Nielsen BMC Bioinformatics 2013, 14:289 (2 October 2013)

Abstract | Provisional PDF

2.

Software   Open Access

BGFit: management and automated fitting of biological growth curves

André Veríssimo, Laura Paixão, Ana Neves, Susana Vinga BMC Bioinformatics 2013, 14:283 (25 September 2013)

Abstract | Full text | PDF | PubMed

3.

Research article   Open Access Highly Accessed

Maximum-parsimony haplotype frequencies inference based on a joint constrained sparse representation of pooled DNA

Guido H Jajamovich, Alexandros Iliadis, Dimitris Anastassiou, Xiaodong Wang BMC Bioinformatics 2013, 14:270 (8 September 2013)

Abstract | Full text | PDF | ePUB | PubMed

4.

Software   Open Access Highly Accessed

inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis

Patrícia Soares, Renato J Alves, Ana B Abecasis, Carlos Penha-Gonçalves, M Gabriela M Gomes, José B Pereira-Leal BMC Bioinformatics 2013, 14:264 (30 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

5.

Software   Open Access Highly Accessed

MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment

Shuying Sun, Aaron Noviski, Xiaoqing Yu BMC Bioinformatics 2013, 14:259 (23 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

6.

Software   Open Access Highly Accessed

A multiple-alignment based primer design algorithm for genetically highly variable DNA targets

Johanna Brodin, Mohan Krishnamoorthy, Gayathri Athreya, Will Fischer, Peter Hraber, Cheryl Gleasner, Lance Green, Bette Korber, Thomas Leitner BMC Bioinformatics 2013, 14:255 (21 August 2013)

Abstract | Full text | PDF | PubMed

7.

Database   Open Access Highly Accessed

Gentrepid V2.0: a web server for candidate disease gene prediction

Sara Ballouz, Jason Y Liu, Richard A George, Naresh Bains, Arthur Liu, Martin Oti, Bruno Gaeta, Diane Fatkin, Merridee A Wouters BMC Bioinformatics 2013, 14:249 (16 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

8.

Software   Open Access Highly Accessed

4273π: Bioinformatics education on low cost ARM hardware

Daniel Barker, David EK Ferrier, Peter WH Holland, John BO Mitchell, Heleen Plaisier, Michael G Ritchie, Steven D Smart BMC Bioinformatics 2013, 14:243 (12 August 2013)

Abstract | Full text | PDF | ePUB | PubMed |  Editor’s summary

An open access, open learning method for teaching bioinformatics uses the Raspberry Pi computer and a custom operating system to teach early-career researchers key skills in systems administration and computational biology at low cost.

9.

Software   Open Access Highly Accessed

RCircos: an R package for Circos 2D track plots

Hongen Zhang, Paul Meltzer, Sean Davis BMC Bioinformatics 2013, 14:244 (10 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

10.

Research article   Open Access Highly Accessed

Classification of protein motifs based on subcellular localization uncovers evolutionary relationships at both sequence and functional levels

Marcos Parras-Moltó, Francisco J Campos-Laborie, Juan García-Diéguez, M Rodríguez-Griñolo, Antonio J Pérez-Pulido BMC Bioinformatics 2013, 14:229 (18 July 2013)

Abstract | Full text | PDF | ePUB | PubMed

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