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Literature DB >> 23727299

GelClust: a software tool for gel electrophoresis images analysis and dendrogram generation.

Sahand Khakabimamaghani¹, Ali Najafi, Reza Ranjbar, Monireh Raam.

Abstract

This paper presents GelClust, a new software that is designed for processing gel electrophoresis images and generating the corresponding phylogenetic trees. Unlike the most of commercial and non-commercial related softwares, we found that GelClust is very user-friendly and guides the user from image toward dendrogram through seven simple steps. Furthermore, the software, which is implemented in C# programming language under Windows operating system, is more accurate than similar software regarding image processing and is the only software able to detect and correct gel 'smile' effects completely automatically. These claims are supported with experiments.

Keywords: Dendrogram; Gel electrophoresis images; Image processing; Phylogenetic trees; Software

Mesh：

Substances：
DNA

Year: 2013 PMID： 23727299 DOI： 10.1016/j.cmpb.2013.04.013

Source DB: PubMed Journal: Comput Methods Programs Biomed ISSN： 0169-2607 Impact factor: 5.428

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Cited

14 in total

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2. A molecular survey of Campylobacter jejuni and Campylobacter coli virulence and diversity.

Authors: Mahdi Ghorbanalizadgan; Bita Bakhshi; Anoshirvan Kazemnejad Lili; Shahin Najar-Peerayeh; Bahram Nikmanesh
Journal: Iran Biomed J Date: 2014-07

3. Automatic DNA Diagnosis for 1D Gel Electrophoresis Images using Bio-image Processing Technique.

Authors: Apichart Intarapanich; Saowaluck Kaewkamnerd; Philip J Shaw; Kittipat Ukosakit; Somvong Tragoonrung; Sissades Tongsima
Journal: BMC Genomics Date: 2015-12-09 Impact factor: 3.969

4. The prevalence of quinolone resistance genes of A, B, S in Escherichia coli strains isolated from three major hospitals in Tehran, Iran.

Authors: Hadis Abbasi; Reza Ranjbar
Journal: Cent European J Urol Date: 2017-01-18

5. The Prevalence of Virulence Genes and Virulotypes of Escherichia coli Strains Isolated from Hospital Wastewaters in Tehran, Iran.

Authors: Reza Ranjbar; Omid Farahani
Journal: Iran J Public Health Date: 2018-05 Impact factor: 1.429

10. Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) Genotyping of Escherichia coli Strains Isolated from Different Animal Stool Specimens.

Authors: Reza Ranjbar; Afsar Tabatabaee; Payam Behzadi; Rohollah Kheiri
Journal: Iran J Pathol Date: 2016-12-29

GelClust: a software tool for gel electrophoresis images analysis and dendrogram generation.

1. Efficacy of BOX-PCR fingerprinting for taxonomic discrimination of bifidobacterial species isolated from diverse sources.

2. A molecular survey of Campylobacter jejuni and Campylobacter coli virulence and diversity.

3. Automatic DNA Diagnosis for 1D Gel Electrophoresis Images using Bio-image Processing Technique.

4. The prevalence of quinolone resistance genes of A, B, S in Escherichia coli strains isolated from three major hospitals in Tehran, Iran.

5. The Prevalence of Virulence Genes and Virulotypes of Escherichia coli Strains Isolated from Hospital Wastewaters in Tehran, Iran.

6. GelJ--a tool for analyzing DNA fingerprint gel images.

7. Molecular typing of uropathogenic E. coli strains by the ERIC-PCR method.

8. Genotypic Diversity of Multidrug Resistant Shigella species from Iran.

Review 9. Bacterial CRISPR Regions: General Features and their Potential for Epidemiological Molecular Typing Studies.

10. Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) Genotyping of Escherichia coli Strains Isolated from Different Animal Stool Specimens.