<i>In silico</i> analysis of complete bacterial genomes: PCR, AFLP–PCR and endonuclease restriction

Bikandi, Joseba; Millán, Rosario San; Rementerı́a, Aitor; Garaizar, Javier

doi:10.1093/bioinformatics/btg491

Cited by 308 publications

(197 citation statements)

References 4 publications

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“…Many SNP- or restriction enzyme-related software tools, such as SNPicker [15], NEBcutter [16], SRP Opt [17], PIRA-PCR Designer [18], SNP cutter [19], SNPselector [20], SNP2CAPS [21], and software for "Restriction of DNA sequences" [22] have been reviewed and compared to SNP-RFLPing (ver. 1) [23].…”

Section: Introductionmentioning

confidence: 99%

SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping

et al. 2010

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BackgroundPCR-restriction fragment length polymorphism (RFLP) assay is a cost-effective method for SNP genotyping and mutation detection, but the manual mining for restriction enzyme sites is challenging and cumbersome. Three years after we constructed SNP-RFLPing, a freely accessible database and analysis tool for restriction enzyme mining of SNPs, significant improvements over the 2006 version have been made and incorporated into the latest version, SNP-RFLPing 2.ResultsThe primary aim of SNP-RFLPing 2 is to provide comprehensive PCR-RFLP information with multiple functionality about SNPs, such as SNP retrieval to multiple species, different polymorphism types (bi-allelic, tri-allelic, tetra-allelic or indels), gene-centric searching, HapMap tagSNPs, gene ontology-based searching, miRNAs, and SNP500Cancer. The RFLP restriction enzymes and the corresponding PCR primers for the natural and mutagenic types of each SNP are simultaneously analyzed. All the RFLP restriction enzyme prices are also provided to aid selection. Furthermore, the previously encountered updating problems for most SNP related databases are resolved by an on-line retrieval system.ConclusionsThe user interfaces for functional SNP analyses have been substantially improved and integrated. SNP-RFLPing 2 offers a new and user-friendly interface for RFLP genotyping that can be used in association studies and is freely available at http://bio.kuas.edu.tw/snp-rflping2.

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Section: Introductionmentioning

confidence: 99%

SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping

et al. 2010

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“…Isolates AMK1, AMJ12, AMT38, AMT39 and AMT43 produced a unique restriction pattern with two fragments of about 220 and 300 bp. These results were confirmed by virtual digesting of their sequences in computer software (Bikandi et al, 2004). These isolates were designated as Group IX.…”

Section: Rflp Profiles Of the Cp Gene From Different Ctv Isolatesmentioning

confidence: 60%

Molecular characterization of Citrus tristeza virus strains in Peninsular Malaysia

Ayazpour¹,

Sijam²,

Vadamalai³

et al. 2011

Afr. J. Microbiol. Res.

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Sixty Malaysian Citrus tristeza virus (CTV) isolates were characterized by bi-directional polymerase chain reaction (BD-PCR) and restriction fragment length polymorphism (RFLP) analysis of their coat protein (CP) gene. In BD-PCR analysis, 392-bp fragments were amplified from seven isolates. The other 53 isolates produced only 320-bp fragments. RFLP patterns of RT-PCR products of CP gene digested with HinfI restriction enzyme were similar to I-IV, VI-VII and two new groups. Isolates AMK1, AMJ12, AMT38, AMT39 and AMT43 could not be classified when they were compared to any standard CTV digest pattern. These isolates produced a unique restriction pattern with two fragments of 210 and 300 bp and isolate AMI61 produced different restriction pattern with three fragments of about 100, 270 and 300 bp. Therefore these isolates were designated as Groups IX and X. These results suggest that CTV populations in Malaysia contain new genetic variants.

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“…The nucleotide variations for each of the genes and the search for differentiating restriction enzymes were determined by means of the Restriction of DNA program (16). These results were confirmed by means of multiple alignment of each allelic pair using the Multalin program, available at www.expasy.org.…”

Section: Determination Of the Allelic Variations And The Search For Smentioning

confidence: 87%

“…Additionally, the CA-MRSA isolates contains genetic mobile elements that give them greater environmental adaptability--as is the case with the arginine catabolic mobile element (ACME), specifically identified in the USA300 clone (21). Clinically, the CA-MRSA isolates have acquired the capacity not only to cause minor infections in healthy persons, but also to cause severe infections such as pneumonia and necrotizing fasciitis (16 (9,10), and the selection supported by a bioinformatics analysis of their location on the genome. In accordance with the genome sequence of the USA300 clone (21), the sek, bsaB, lukF-PV/lukS-PV genes are found on different mobile genetic elements.…”

Section: Discussionmentioning

confidence: 99%

Diseño de dos metodologías moleculares para la rápida identificación de aislamientos de Staphylococcus aureus resistente a meticilina asociados a la comunidad en Colombia

et al. 2012

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In silico analysis of complete bacterial genomes: PCR, AFLP–PCR and endonuclease restriction

Abstract: This is a new molecular biology resource freely available over the Internet at http://www.in-silico.com

Cited by 308 publications

References 4 publications

SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping

SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping

Molecular characterization of Citrus tristeza virus strains in Peninsular Malaysia

Diseño de dos metodologías moleculares para la rápida identificación de aislamientos de Staphylococcus aureus resistente a meticilina asociados a la comunidad en Colombia

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