scholarly journals Significance Tests and Weighted Values for AFLP Similarities, Based on Arabidopsis in Silico AFLP Fragment Length Distributions

Genetics ◽  
2004 ◽  
Vol 167 (4) ◽  
pp. 1915-1928 ◽  
Author(s):  
Wim J. M. Koopman ◽  
Gerrit Gort
Keyword(s):  
Fragment Length ◽  
In Silico ◽  
Significance Tests ◽  
Aflp Fragment ◽  
Weighted Values

scholarly journals 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

2005 ◽  
Vol 71 (3) ◽  
pp. 1671-1673 ◽  
Author(s):  
Peter Ricke ◽  
Steffen Kolb ◽  
Gesche Braker
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Forest Soil ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
In Silico ◽  
Fragment Length Polymorphism ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Restriction Fragment Length

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.

In silico analysis of a putative SPIRAL gene related to strawberry ripening

2010 ◽  
Vol 58 (3) ◽  
pp. 267-272
Author(s):  
D. Polgári ◽  
B. Kalapos ◽  
V. Tisza ◽  
L. Kovács ◽  
B. Kerti ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Cdna Fragment ◽  
Nucleotide Level ◽  
Gene Group ◽  
Climacteric Fruit ◽  
Ripening Stages ◽  
Fruit Development And Ripening ◽  
Aflp Fragment ◽  
Silico Analysis

The aim of this study was to characterize a gene associated with ripening in strawberry, a non-climacteric fruit. Differently expressed transcripts of candidate genes functioning in fruit development and ripening were identified from strawberry ( Fragaria × ananassa Duch.) in four ripening stages using the cDNA-AFLP method. The cDNA fragment designated C11M32M003 was selected from the putative ripening-related genes for further analysis. This transcript accumulated in the green receptacle, and the achene, but gene expression decreased in both tissues in parallel with the progress of ripening (Balogh, 2006). In silico analysis revealed that both the cDNA-AFLP fragment (C11M32M003) and the full-length cDNA AY695666 showed over 60% homology at the nucleotide level with two gene groups found in various plant species, including Arabidopsis thaliana . One of the candidate groups consisted of NITRILASE sequences thought to be related to auxin biosynthesis. As an alternative, a lesser known gene group named SPIRAL was suggested. The results of the detailed bioinformatic comparisons presented in this paper prove that the strawberry sequence analysed belongs to the SPIRAL gene family.

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

2021 ◽  
Vol 9 (1) ◽  
pp. 29
Author(s):  
Kevin Timbuleng ◽  
Beivy J Kolondam ◽  
Deidy Katili
Keyword(s):  
Polymerase Chain Reaction ◽  
Restriction Fragment Length Polymorphism ◽  
Length Polymorphism ◽  
Fragment Length ◽  
In Silico ◽  
Fragment Length Polymorphism ◽  
Chain Reaction ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Restriction Fragment Length

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

scholarly journals Amplified fragment length homoplasy: in silico analysis for model and non-model species

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 287 ◽  
Author(s):  
Margot Paris ◽  
Benjamin Bonnes ◽  
Gentile Francesco Ficetola ◽  
Benedicte N Poncet ◽  
Laurence Despres
Keyword(s):  
Fragment Length ◽  
In Silico ◽  
In Silico Analysis ◽  
Model Species ◽  
Silico Analysis

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

2021 ◽  
Author(s):  
Abhijeet Singh
Keyword(s):  
User Interface ◽  
Restriction Fragment Length Polymorphism ◽  
Graphical User Interface ◽  
Length Polymorphism ◽  
Fragment Length ◽  
In Silico ◽  
Fragment Length Polymorphism ◽  
Restriction Digestion ◽  
Genome Sequences ◽  
Restriction Fragment Length

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.

Approximating power for significance tests with one degree of freedom.

1997 ◽  
Vol 2 (2) ◽  
pp. 186-191 ◽  
Author(s):  
William P. Dunlap ◽  
Leann Myers
Keyword(s):  
Degree Of Freedom ◽  
Significance Tests
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