REDigest: a Python GUI for In-Silico Restriction Digestion Analysis of Genes or Complete Genome Sequences

Graphical User Interface ◽

Length Polymorphism ◽

Fragment Length ◽

In Silico ◽

Restriction Digestion ◽

Genome Sequences ◽

Restriction fragment length polymorphism (RFLP) is a technology for the molecular characterization of DNA and widely used genome mapping, medical genetics, molecular microbiology and forensics etc. Terminal restriction fragment length polymorphism (T-RFLP), a variant of RFLP is extensively used in environmental microbiology for the microbial community profiling based on the restriction digestion profile of marker gene (16S rRNA, FTHFS etc.) amplicons. At present, there is a lack of a tool which can perform in-silico restriction digestion of a large number of sequences at a time, in an interactive way and as an output produce sequences of the restriction fragments and visualization plot. I have developed a graphical user interface based software REDigest for the in-silico restriction digestion analysis for gene or genome sequences. The REDigest software program with a graphical user interface is freely available at https://github.com/abhijeetsingh1704/REDigest.

Application of a Newly Developed ARB Software-Integrated Tool for In Silico Terminal Restriction Fragment Length Polymorphism Analysis Reveals the Dominance of a Novel pmoA Cluster in a Forest Soil

Applied and Environmental Microbiology ◽

10.1128/aem.71.3.1671-1673.2005 ◽

2005 ◽

Vol 71 (3) ◽

pp. 1671-1673 ◽

Cited By ~ 66

Author(s):

Peter Ricke ◽

Steffen Kolb ◽

Gesche Braker

Keyword(s):

Forest Soil ◽

Restriction Fragment ◽

Length Polymorphism ◽

Fragment Length ◽

In Silico ◽

Rrna Gene ◽

Polymorphism Analysis ◽

ABSTRACT TRF-CUT, an ARB-implemented tool, was developed to predict in silico the terminal restriction fragments of aligned small-subunit rRNA gene or functional gene sequences. Application of this new tool to perform directed terminal restriction fragment length polymorphism analysis of pmoA products obtained from a forest soil revealed that novel cluster I methanotrophic bacteria were dominant.

Identification of a Cucumber mosaic virus Isolate from Passiflora edulis in Southern Italy and Validation of Subgroup Identification by In Silico Restriction Fragment Length Polymorphism

Journal of Phytopathology ◽

10.1111/j.1439-0434.2009.01604.x ◽

2009 ◽

Vol 157 (11-12) ◽

pp. 762-767 ◽

Cited By ~ 1

Author(s):

Giuseppe Parrella ◽

Daniela Sorrentino

Keyword(s):

Length Polymorphism ◽

Fragment Length ◽

In Silico ◽

Virus Isolate ◽

Southern Italy ◽

Passiflora Edulis ◽

Subgroup Identification ◽

PCR-RFLP Design for Authentication of Red Snapper Species Based on CYB Gene

JURNAL ILMIAH PLATAX ◽

10.35800/jip.9.1.2021.33541 ◽

2021 ◽

Vol 9 (1) ◽

pp. 29

Author(s):

Kevin Timbuleng ◽

Beivy J Kolondam ◽

Deidy Katili

Keyword(s):

Polymerase Chain Reaction ◽

Length Polymorphism ◽

Fragment Length ◽

In Silico ◽

Chain Reaction ◽

Pcr Rflp ◽

Polymerase Chain ◽

The PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) technique is a species identification method that can facilitate food inspection agencies to overcome mislabelling. In addition, this technique is simple, fast, powerful, and cheap compared to DNA barcodes. This study aimed to accommodate the problem in determining restriction endonuclease enzymes for the digestion of PCR end products through the design of snapper species authentication using the CYB gene in silico. Differentiation of CYB gene sequences with DNA barcoding showed that all species could be differentiated with the highest similarity level in Red Fish (Sebastes) species by 98.9% and snapper species between L. malabaricus and L. erythropterus by 99.8%. Enzyme tracing based on sequences variation of snapper species with substitution species found three potential enzymes from the CYB gene sequence, namely, Accl, Fnu4HI, and Tsp45I. Where all these enzymes can discriminate red snapper species among other.Key words: PCR-RFLP; CYB gene; Red snapperAbstrakTeknik PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) merupakan metode identifikasi spesies yang dapat memfasilitasi lembaga inspeksi makanan untuk mengatasi mislabelling. Selain itu, teknik ini sederhana, cepat, kuat, dan murah dibandingkan dengan barcode DNA. Penelitian ini bertujuan untuk mengakomodasi masalah dalam menentukan enzim restriksi endonuklease untuk digesti produk akhir PCR lewat perancangan autentikasi spesies ikan kakap menggunakan gen CYB secara in silico. Diferensiasi sekuens gen CYB dengan DNA barcoding menunjukkan semua spesies dapat dibedakan dengan tingkat kesamaan tertinggi pada spesies Red Fish (Sebastes) sebesar 98,9% dan spesies kakap antara L. malabaricus dan L. erythropterus sebesar 99,8%. Penelusuran enzim berdasarkan variasi sekuens spesies kakap dengan spesies substitusi ditemukan sebanyak tiga enzim yang berpotensi yaitu, Accl, Fnu4HI, dan Tsp45I. Semua enzim tersebut dapat memdiskriminasikan spesies kakap merah dari spesies lainnya.Kata kunci: PCR-RFLP; gen CYB; ikan kakap merah