Comparative analysis of the cattle and human genomes: detection of ZOO-FISH and gene mapping-based chromosomal homologies

1996 ◽  
Vol 7 (4) ◽  
pp. 297-302 ◽  
Author(s):  
B. P. Chowdhary ◽  
L. Frönicke ◽  
I. Gustavsson ◽  
H. Scherthan
Keyword(s):  
Comparative Analysis ◽  
Gene Mapping ◽  
Human Genomes ◽  
Chromosomal Homologies

A comparative map of the porcine and human genomes demonstrates ZOO-FISH and gene mapping-based chromosomal homologies

1996 ◽  
Vol 7 (4) ◽  
pp. 285-290 ◽  
Author(s):  
L. Frönicke ◽  
B. P. Chowdhary ◽  
H. Scherthan ◽  
I. Gustavsson
Keyword(s):  
Gene Mapping ◽  
Comparative Map ◽  
Human Genomes ◽  
Chromosomal Homologies

scholarly journals A Comparative Analysis of L1 Retrotransposition Activities in Human Genomes Suggests an Ongoing Increase in L1 Number Despite an Evolutionary Trend Towards Lower Activity

2021 ◽  
Author(s):  
Sawsan Sami Wehbi ◽  
Heinrich zu Dohna
Keyword(s):  
Cell Culture ◽  
Population Dynamics ◽  
Comparative Analysis ◽  
Transposable Elements ◽  
Human Population ◽  
Population Level ◽  
Evolutionary Trend ◽  
Human Genomes ◽  
Long Interspersed Nuclear Elements ◽  
Insight Into

Abstract BackgroundLINE-1 (Long Interspersed Nuclear Elements, L1) retrotransposons are the only autonomously active transposable elements in the human genome. The evolution of L1 retrotransposition rates and its implications for L1 dynamics are poorly understood. Retrotransposition rates are commonly measured in cell culture-based assays, but it is unclear how well these measurements provide insight into L1 population dynamics. This study applied comparative methods to estimate parameters for the evolution of retrotransposition rates, and infer L1 dynamics from these estimates.ResultsOur results show that the rates at which new L1s emerge in the human population correlate positively to cell-culture based retrotransposition activities, that there is an evolutionary trend towards lower retrotransposition activity, and that this evolutionary trend is not sufficient to counter-balance the increase in L1s resulting from continuing retrotransposition. ConclusionsTogether, these findings support a model of the population-level L1 retrotransposition dynamics that is consistent with prior expectations and indicate the remaining gaps in the understanding of L1 dynamics in human genomes.

scholarly journals A 1.5-Mb-resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes

Genomics ◽  
2007 ◽  
Vol 89 (2) ◽  
pp. 189-196 ◽  
Author(s):  
William J. Murphy ◽  
Brian Davis ◽  
Victor A. David ◽  
Richa Agarwala ◽  
Alejandro A. Schäffer ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Radiation Hybrid ◽  
Human Genomes ◽  
Radiation Hybrid Map

scholarly journals A comparative analysis of L1 retrotransposition activities in human genomes suggests an ongoing increase in L1 number despite an evolutionary trend towards lower activity

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sawsan Sami Wehbi ◽  
Heinrich zu Dohna
Keyword(s):  
Cell Culture ◽  
Population Dynamics ◽  
Comparative Analysis ◽  
Transposable Elements ◽  
Human Population ◽  
Population Level ◽  
Evolutionary Trend ◽  
Human Genomes ◽  
Long Interspersed Nuclear Elements ◽  
Insight Into

Abstract Background LINE-1 (Long Interspersed Nuclear Elements, L1) retrotransposons are the only autonomously active transposable elements in the human genome. The evolution of L1 retrotransposition rates and its implications for L1 dynamics are poorly understood. Retrotransposition rates are commonly measured in cell culture-based assays, but it is unclear how well these measurements provide insight into L1 population dynamics. This study applied comparative methods to estimate parameters for the evolution of retrotransposition rates, and infer L1 dynamics from these estimates. Results Our results show that the rates at which new L1s emerge in the human population correlate positively to cell-culture based retrotransposition activities, that there is an evolutionary trend towards lower retrotransposition activity, and that this evolutionary trend is not sufficient to counter-balance the increase in active L1s resulting from continuing retrotransposition. Conclusions Together, these findings support a model of the population-level L1 retrotransposition dynamics that is consistent with prior expectations and indicate the remaining gaps in the understanding of L1 dynamics in human genomes.

scholarly journals Tandemly repeated trinucleotides - comparative analysis.

2006 ◽  
Vol 53 (2) ◽  
pp. 279-287 ◽  
Author(s):  
Monika Piwowar ◽  
Jan Meus ◽  
Piotr Piwowar ◽  
Zdzisław Wiśniowski ◽  
Justyna Stefaniak ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Neurodegenerative Diseases ◽  
Rattus Norvegicus ◽  
High Frequency ◽  
Homo Sapiens ◽  
Trinucleotide Repeats ◽  
The Other ◽  
Sequence Motifs ◽  
Human Genomes ◽  
Coefficient Method

Characteristics of 64 possible tandem trinucleotide repeats (TSSR) from Homo sapiens (hs), Mus musculus (mm) and Rattus norvegicus (rn) genomes are presented. Comparative analysis of TSSR frequency depending on their repetitiveness and similarity of the TSSR length distributions is shown. Comparative analysis of TSSR sequence motifs and association between type of motif and its length (n) using rho-coefficient method (quantitatively measuring the association between variables in contingency tables) is presented. These analyses were carried out in the context of neurodegenerative diseases based on trinucleotide tandems. The length of these tandems and their relation to other TSSR is estimated. It was found that the higher repetitiveness (n) the lower frequency of trinucleotides tandems. Differences between genomes under consideration, especially in longer than n=9 TSSR were discussed. A significantly higher frequency off A- and T-rich tandems is observed in the human genome (as well as in human mRNA). This observation also applies to mm and rn, although lower abundant in proportion to human genomes was found. The origin of elongation (or shortening) of TSSR seems to be neither frequency nor length dependent. The results of TSSR analysis presented in this work suggest that neurodegenerative disease-related microsatellites do not differ versus the other except the lower frequency versus the other TSSR. CAG occurs with relatively high frequency in human mRNA, although there are other TSSR with higher frequency that do not cause comparable disease disorders. It suggests that the mechanism of TSSR instability is not the only origin of neurodegenerative diseases.

scholarly journals Comparative assessments of indel annotations in healthy and cancer genomes with next-generation sequencing data

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Jing Chen ◽  
Jun-tao Guo
Keyword(s):  
Comparative Analysis ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Evaluation Approach ◽  
Insertion And Deletion ◽  
Human Genomes ◽  
Indel Calling ◽  
Major Variation ◽  
Improved Performance ◽  
Performance Comparisons

Abstract Background Insertion and deletion (indel) is one of the major variation types in human genomes. Accurate annotation of indels is of paramount importance in genetic variation analysis and investigation of their roles in human diseases. Previous studies revealed a high number of false positives from existing indel calling methods, which limits downstream analyses of the effects of indels on both healthy and disease genomes. In this study, we evaluated seven commonly used general indel calling programs for germline indels and four somatic indel calling programs through comparative analysis to investigate their common features and differences and to explore ways to improve indel annotation accuracy. Methods In our comparative analysis, we adopted a more stringent evaluation approach by considering both the indel positions and the indel types (insertion or deletion sequences) between the samples and the reference set. In addition, we applied an efficient way to use a benchmark for improved performance comparisons for the general indel calling programs Results We found that germline indels in healthy genomes derived by combining several indel calling tools could help remove a large number of false positive indels from individual programs without compromising the number of true positives. The performance comparisons of somatic indel calling programs are more complicated due to the lack of a reliable and comprehensive benchmark. Nevertheless our results revealed large variations among the programs and among cancer types. Conclusions While more accurate indel calling programs are needed, we found that the performance for germline indel annotations can be improved by combining the results from several programs. In addition, well-designed benchmarks for both germline and somatic indels are key in program development and evaluations.

Comparative analysis of processed pseudogenes in the mouse and human genomes

2004 ◽  
Vol 20 (2) ◽  
pp. 62-67 ◽  
Author(s):  
Zhaolei Zhang ◽  
Nick Carriero ◽  
Mark Gerstein
Keyword(s):  
Comparative Analysis ◽  
Human Genomes ◽  
Processed Pseudogenes
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