scholarly journals Computational Comparative Genomics of Eu- and Prokaryotes

2002 ◽  
Vol 3 (2) ◽  
pp. 167-168
Author(s):  
Clemens Suter-Crazzolara ◽  
Günther Kurapkat
Keyword(s):  
Comparative Genomics ◽  
Computational Comparative Genomics

scholarly journals Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms

Gene ◽  
2006 ◽  
Vol 365 ◽  
pp. 11-20 ◽  
Author(s):  
Jianxin Wang ◽  
Lei Song ◽  
M. Katherine Gonder ◽  
Sami Azrak ◽  
David A. Ray ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Whole Genome ◽  
Alu Insertion ◽  
Computational Comparative Genomics ◽  
Alu Insertion Polymorphisms

scholarly journals PLATCOM: a Platform for Computational Comparative Genomics

2005 ◽  
Vol 21 (10) ◽  
pp. 2514-2516 ◽  
Author(s):  
K. Choi ◽  
Y. Ma ◽  
J.-H. Choi ◽  
S. Kim
Keyword(s):  
Comparative Genomics ◽  
Computational Comparative Genomics

scholarly journals Correction to: A high-quality cucumber genome assembly enhances computational comparative genomics

2020 ◽  
Vol 295 (2) ◽  
pp. 535-535
Author(s):  
Paweł Osipowski ◽  
Magdalena Pawełkowicz ◽  
Michał Wojcieszek ◽  
Agnieszka Skarzyńska ◽  
Zbigniew Przybecki ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Genome Assembly ◽  
High Quality ◽  
Cucumber Genome ◽  
Computational Comparative Genomics

scholarly journals A high-quality cucumber genome assembly enhances computational comparative genomics

2019 ◽  
Vol 295 (1) ◽  
pp. 177-193 ◽  
Author(s):  
Paweł Osipowski ◽  
Magdalena Pawełkowicz ◽  
Michał Wojcieszek ◽  
Agnieszka Skarzyńska ◽  
Zbigniew Przybecki ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Real Time ◽  
Single Molecule ◽  
Prediction Method ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Cucumber Genome ◽  
Genome Dynamics ◽  
Genome Draft ◽  
Computational Comparative Genomics

Abstract Genetic variation is expressed by the presence of polymorphisms in compared genomes of individuals that can be transferred to next generations. The aim of this work was to reveal genome dynamics by predicting polymorphisms among the genomes of three individuals of the highly inbred B10 cucumber (Cucumis sativus L.) line. In this study, bioinformatic comparative genomics was used to uncover cucumber genome dynamics (also called real-time evolution). We obtained a new genome draft assembly from long single molecule real-time (SMRT) sequencing reads and used short paired-end read data from three individuals to analyse the polymorphisms. Using this approach, we uncovered differentiation aspects in the genomes of the inbred B10 line. The newly assembled genome sequence (B10v3) has the highest contiguity and quality characteristics among the currently available cucumber genome draft sequences. Standard and newly designed approaches were used to predict single nucleotide and structural variants that were unique among the three individual genomes. Some of the variant predictions spanned protein-coding genes and their promoters, and some were in the neighbourhood of annotated interspersed repetitive elements, indicating that the highly inbred homozygous plants remained genetically dynamic. This is the first bioinformatic comparative genomics study of a single highly inbred plant line. For this project, we developed a polymorphism prediction method with optimized precision parameters, which allowed the effective detection of small nucleotide variants (SNVs). This methodology could significantly improve bioinformatic pipelines for comparative genomics and thus has great practical potential in genomic metadata handling.

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