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SNP-VISTA: an interactive SNP visualization tool

Nameeta Shah, Michael V Teplitsky, Simon Minovitsky, Len A Pennacchio, Philip Hugenholtz, Bernd Hamann, Inna L Dubchak
2005 BMC Bioinformatics  
Massive amounts of ecogenomics data for studying homologous recombination in microbial populations (EcoSNP-VISTA).  ...  We have developed and present two modifications of an interactive visualization tool, SNP-VISTA, to aid in the analyses of the following types of data: A.  ...  EcoSNP-VISTA provides insight into homologous recombination in microbial populations and has the potential to guide in the development of computational methods for such analysis.  ... 
doi:10.1186/1471-2105-6-292 pmid:16336665 pmcid:PMC1325058 fatcat:3unnorax3ne2ffu25qtng6s7lu

SimPlot++: a Python application for representing sequence similarity and detecting recombination [article]

Stéphane Samson, Étienne Lord, Vladimir Makarenkov
2022 arXiv   pre-print
Motivation: Accurate detection of sequence similarity and homologous recombination are essential parts of many evolutionary analyses.  ...  events using Phi, Max-X2, NSS or proportion tests, and to generate and analyze interactive sequence similarity networks.  ...  Circoletto: visualizing sequence similarity with Circos, Bioinformatics, 26, 2620-2621.  ... 
arXiv:2112.09755v2 fatcat:icayhnbkefa45mukijlqxj5uaa

Computational Resources in Infectious Disease: Limitations and Challenges

Eva C. Berglund, Björn Nystedt, Siv G. E. Andersson, Ernest Fraenkel
2009 PLoS Computational Biology  
With the expected huge increase of complete and draft genomes for many strains of a species, there is a need for programs capable of screening a large set of alignments for recombination signals, with  ...  New methods for analyzing evolution by recombination. Improved models and visualization tools are needed to analyze recombination.  ... 
doi:10.1371/journal.pcbi.1000481 pmid:19855825 pmcid:PMC2756590 fatcat:c7riyirl3feave4lchtlb3wwpy

VIEWpoly: a visualization tool to integrate and explore results of polyploid genetic analysis

Cristiane Hayumi Taniguti, Gabriel de Siqueira Gesteira, Jeekin Lau, Guilherme da Silva Pereira, Zhao-Bang Zeng, David Byrne, Oscar Riera-Lizarazu, Marcelo Mollinari
2022 Journal of Open Source Software  
VIEWpoly is an R package for visualizing, exploring, and integrating results from different polyploid computational tools using an interactive graphical user interface.  ...  The package allows users to explore linkage and QTL analysis results and integrates these with genomic information in a genome browser, facilitating the search for candidate genes.  ...  The module highlights all linkage groups in a graphical representation with their respective marker positions and estimated recombination fractions, allowing for a direct comparison between homology groups  ... 
doi:10.21105/joss.04242 fatcat:lhgjdqdjwfgdthg6culqjowpye

TreeMos: a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism

J. D. Moore, R. G. Allaby
2008 Computer applications in the biosciences : CABIOS  
Data sets can include whole genome sequences allowing phylogenomic analyses in which mosaicism may be attributed to recombination between any two points in the genome.  ...  TreeMos uses a sliding window and local alignment algorithm to identify the nearest neighbour of each sequence segment, and visualizes instances of sequence segments whose nearest neighbour is anomalous  ...  segments (through recombination) in otherwise non-homologous sequences.  ... 
doi:10.1093/bioinformatics/btn027 pmid:18204056 fatcat:cykm3ers65evdfqx4q2qtzfq7y

A framework for stochastic simulations and visualization of biological electron-transfer dynamics

C. Masato Nakano, Hye Suk Byun, Heng Ma, Tao Wei, Mohamed Y. El-Naggar
2015 Computer Physics Communications  
Starting from X-ray crystal structures of the constituent cytochromes, molecular dynamics simulations are combined with homology modeling, protein docking, and binding free energy computations to sample  ...  VizBET has been used to reveal the nature of ET dynamics associated with novel nonequilibrium phase transitions in a candidate configuration of the Mtr-Omc complex due to electron-electron interactions  ...  Acknowledgments The authors are grateful for insightful discussions with Dr. Liang  ... 
doi:10.1016/j.cpc.2015.03.009 fatcat:4bsvf4moyfdbhho5rbsojflywa

3dSS: 3D structural superposition

K. Sumathi, P. Ananthalakshmi, M. N. A. Md. Roshan, K. Sekar
2006 Nucleic Acids Research  
The molecular visualization tool RASMOL is interfaced with the server to visualize the superposed 3D structures with the water molecules (invariant or common) in the client machine.  ...  3dSS is a web-based interactive computing server, primarily designed to aid researchers, to superpose two or several 3D protein structures.  ...  ACKNOWLEDGEMENTS The corresponding author (K.S.) thanks Dr Geoffrey Barton and Dr Andrew Martin for permitting to use their superposition programs in the computing server. The authors thank Ch.  ... 
doi:10.1093/nar/gkl036 pmid:16844975 pmcid:PMC1538824 fatcat:rhfjmq7ugvg3bjv6tdwuhcfq7u

Interactome Analysis and Docking Sites of MutS Homologs Reveal New Physiological Roles in Arabidopsis thaliana

Mohamed Ragab AbdelGawwad, Aida Marić, Abdullah Ahmed Al-Ghamdi, Ashraf A. Hatamleh
2019 Molecules  
The MSH homologs extensively interacted with both TIL1 and TIL2 (DNA polymerase epsilon catalytic subunit), proteins involved in cell fate determination during plant embryogenesis and involved in flowering  ...  Additionally, interactions with the RECQ protein family (helicase enzymes) and proteins of nucleotide excision repair pathway were detected.  ...  In 2004, when it was published, ClusPro was first a completely automated program for computational protein docking.  ... 
doi:10.3390/molecules24132493 fatcat:6hu3anmquvdqnimipvmzqyjsgm

The Rad51 and Dmc1 recombinases: a non-identical twin relationship

Jean-Yves Masson, Stephen C West
2001 TIBS -Trends in Biochemical Sciences. Regular ed  
The answers to these questions lie in understanding the basis of meiotic recombination, the process that leads to genetic variation.  ...  The alignments were made using the program Gap of the Genetics Computer Group.  ...  Protein-DNA complexes were visualized after negative staining with uranyl acetate.  ... 
doi:10.1016/s0968-0004(00)01742-4 pmid:11166572 fatcat:33nb5gslafdudmvifxpkhk6ahu

Identifying functional groups among the diverse, recombining antigenic var genes of the malaria parasite Plasmodium falciparum from a local community in Ghana

Mary M. Rorick, Edward B. Baskerville, Thomas S. Rask, Karen P. Day, Mercedes Pascual, Roland R. Regoes
2018 PLoS Computational Biology  
Instead, it infers functional similarity among recombining parts based on the sharing of similar co-occurrence interactions with other parts.  ...  PLOS Computational Biology | https://doi.  ...  Lastly, we would like to thank laboratory personnel at New York University and The University of Melbourne for their assistance with laboratory experiments.  ... 
doi:10.1371/journal.pcbi.1006174 pmid:29897905 pmcid:PMC6016947 fatcat:3inya6nxwnhbrhm5vitkye46je

Positive regulation of general transcription factor SIII by a tailed ubiquitin homolog

K. P. Garrett, T. Aso, J. N. Bradsher, S. I. Foundling, W. S. Lane, R. C. Conaway, J. W. Conaway
1995 Proceedings of the National Academy of Sciences of the United States of America  
Here we report molecular cloning and biochemical characterization of the Sll p18 subunit, which is found to be a member of the ubiquitin homology (UbH) gene family and functions as a positive regulatory  ...  The model was constructed by conservative molecular modeling using a ubiquitin homology template and geometric regularization with the LORE program (Version 2.2) (50).  ...  Sequences were aligned by using the BESTFIT program of the Genetics Computer Group package (36) . l, Identical residues;: and , residues with alignment scores (36) .0.5 and .0.1, respectively.  ... 
doi:10.1073/pnas.92.16.7172 pmid:7638163 pmcid:PMC41301 fatcat:fm6ny2zafvb7rpxwwga4bgbauy

Page 986 of Genetics Vol. 173, Issue 2 [page]

2006 Genetics  
Finally, we used the interactive MACAW program (SCHULER ef al. 1991) to visualize and precisely define the conserved blocks.  ...  ClustalW and ClustalX programs generated multiple sequence alignments with some minor manual adjustments for Macintosh iBook computer.  ... 

DNA Sequence Alignment during Homologous Recombination

Eric C. Greene
2016 Journal of Biological Chemistry  
A key facet of homologous recombination is the ability of recombination proteins to perfectly align the damaged DNA with homologous sequence located elsewhere in the genome.  ...  , respectively, with amino acid sequence homology to RecA.  ...  Initial experiments revealed that homologous pairing interactions could only be detected with dsDNA molecules that were tethered by one end to the sample chamber surface (no homologous pairing interactions  ... 
doi:10.1074/jbc.r116.724807 pmid:27129270 pmcid:PMC4882428 fatcat:ohpeggpy75aj5lsdzsnlgsqk6a

GT-Miner: a graph-theoretic data miner, viewer, and model processor

Douglas E. Brown, Amy J. Powell, Ignazio Carbone, Ralph A. Dean
2008 Bioinformation  
GT-Miner is designed for visual data analysis and mining operations, interacts with other software, including databases, and works with diverse data types.  ...  Inexpensive computational power combined with high-throughput experimental platforms has created a wealth of biological information requiring analytical tools and techniques for interpretation.  ...  The GUI supports user interactivity and graph visualization through multiple visual layouts, as well as multiple transformations for element filtering, merging of labeled graphs, and cluster analysis.  ... 
doi:10.6026/97320630003235 pmid:19255640 pmcid:PMC2646195 fatcat:y3rjh7ck2vdgbpgk3bw6ayfmbq

Sequences of five potential recombination sites encoded close to an immunoglobulin kappa constant region gene

E. E. Max, J. G. Seidman, P. Leder
1979 Proceedings of the National Academy of Sciences of the United States of America  
The J segments also display striking sequence homology to one another in both their coding and immediately flanking sequences.  ...  Immunoglobulin K chain gene formation involves site-specific somatic recombination between one of several hundred germ-line variable region genes and a joining site (or "J segment") encoded close to the  ...  Maizel, Jr., for his assistance in establishing the computer programs used in these studies and to Dr.  ... 
doi:10.1073/pnas.76.7.3450 pmid:115000 pmcid:PMC383843 fatcat:iu2ftkfkgzeulb77drzq3wh2uy
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