Results 31 to 40 of about 1,691,339 (303)

Prospects of pan-genomics in barley

Theoretical and Applied Genetics, 2018
The concept of a pan-genome refers to intraspecific diversity in genome content and structure, encompassing both genes and intergenic space. Pan-genomic studies employ a combination of de novo sequence assembly and reference-based alignment to discover and genotype structural variants.
Cécile Monat, Mona Schreiber, Nils Stein, Martin Mascher   +3 more
openaire   +3 more sources

PGAP: pan-genomes analysis pipeline [PDF]

Bioinformatics, 2011
Abstract Summary: With the rapid development of DNA sequencing technology, increasing bacteria genome data enable the biologists to dig the evolutionary and genetic information of prokaryotic species from pan-genome sight. Therefore, the high-efficiency pipelines for pan-genome analysis are mostly needed.
Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jing-Fa Xiao, Jun Yu 0004   +5 more
openaire   +2 more sources

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Nature Communications, 2020
With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes
Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Gordon Saksena, Kyle Ellrott, Michael C. Wendl, David A. Wheeler, Gad Getz, Jared T. Simpson, Mark B. Gerstein, Li Ding, PCAWG Consortium   +20 more
doaj   +1 more source

Calculating orthologs in bacteria and archaea : a divide and conquer approach [PDF]

, 2011
Among proteins, orthologs are defined as those that are derived by vertical descent from a single progenitor in the last common ancestor of their host organisms.
Loman Nicholas J., Nicholas J Loman, Mihail R. Halachev, Halachev, Mihail, Pallen, Mark J., Mark J. Pallen, Mihail R Halachev, Loman, Nicholas J., Halachev Mihail R., Halachev, Mihail R., Pallen Mark J., Loman, Nicholas, Pallen, Mark, Nicholas J. Loman, Mark J Pallen   +14 more
core   +1 more source

Pan-genome gene family distribution.

, 2022
(A) The pan-genome of 260 A. fumigatus strains included 15,508 gene families in total, including 8,595 (55.42%) core genes (present in >95% of strains), 3,660 (23.60%) accessory genes (present in >2 and (B) The distribution of the number of genomes ...
Lotus A. Lofgren (9253428), Brandon S. Ross (14135875), Robert A. Cramer (8844023), Jason E. Stajich (6700331)   +3 more
core   +1 more source

Towards the Complete Goat Pan-Genome by Recovering Missing Genomic Segments From the Reference Genome

Frontiers in Genetics, 2019
It is broadly expected that next generation sequencing will ultimately generate a complete genome as is the latest goat reference genome (ARS1), which is considered to be one of the most continuous assemblies in livestock.
Ran Li, Weiwei Fu, Rui Su, Xiaomeng Tian, Duo Du, Yue Zhao, Zhuqing Zheng, Qiuming Chen, Shan Gao, Yudong Cai, Xihong Wang, Jinquan Li, Yu Jiang   +12 more
doaj   +1 more source

A super pan-genomic landscape of rice

Cell Research, 2022
AbstractPan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice.
Lianguang Shang, Xiaoxia Li, Huiying He, Qiaoling Yuan, Yanni Song, Zhaoran Wei, Hai Lin, Min Hu, Fengli Zhao, Chao Zhang, Yuhua Li, Hongsheng Gao, Tianyi Wang, Xiangpei Liu, Hong Zhang, Ya Zhang, Shuaimin Cao, Xiaoman Yu, Bintao Zhang, Yong Zhang, Yiqing Tan, Mao Qin, Cheng Ai, Yingxue Yang, Bin Zhang, Zhiqiang Hu, Hongru Wang, Yang Lv, Yuexing Wang, Jie Ma, Quan Wang, Hongwei Lu, Zhe Wu, Shanlin Liu, Zongyi Sun, Hongliang Zhang, Longbiao Guo, Zichao Li, Yongfeng Zhou, Jiayang Li, Zuofeng Zhu, Guosheng Xiong, Jue Ruan, Qian Qian   +43 more
openaire   +2 more sources

Efficient oligonucleotide probe selection for pan-genomic tiling arrays

BMC Bioinformatics, 2009
Background Array comparative genomic hybridization is a fast and cost-effective method for detecting, genotyping, and comparing the genomic sequence of unknown bacterial isolates.
Zhang Wei, Deng Xiangyu, Phillippy Adam M, Salzberg Steven L   +3 more
doaj   +1 more source

Pan-genome analysis of Seep-SRB1a metagenomes.

, 2023
Fourteen genomes from nine Seep-SRB1a species were analyzed using the Anvi’o pan-genome analysis pipeline [45]. Five gene cluster bins were annotated based on genes that were identified as part of the core metagenome, unique to Seep-SRB1a sp.
Danielle Goudeau (8455311), Rex R. Malmstrom (8615046), Tanja Woyke (111784), Hang Yu (278278), Fabai Wu (17041703), Kyle S. Metcalfe (17041706), Victoria J. Orphan (3944372), Antoine Crémière (17041709), Ranjani Murali (17041700), Daan R. Speth (5548529), Rafael Laso-Pèrez (17041712), Grayson L. Chadwick (11910062), Roland Hatzenpichler (487768), Stephanie A. Connon (17041715)   +13 more
core   +1 more source

Getting insight into the pan-genome structure with PangTree

BMC Genomics, 2020
Background The term pan-genome was proposed to denominate collections of genomic sequences jointly analyzed or used as a reference. The constant growth of genomic data intensifies development of data structures and algorithms to investigate pan-genomes ...
Paulina Dziadkiewicz, Norbert Dojer
doaj   +1 more source