Zobrazeno 1 - 10
of 63
pro vyhledávání: '"Optical maps"'
Autor:
Bin Huang, Guozheng Wei, Bing Wang, Fusong Ju, Yi Zhong, Zhuozheng Shi, Shiwei Sun, Dongbo Bu
Publikováno v:
BMC Bioinformatics, Vol 22, Iss 1, Pp 1-17 (2021)
Abstract Background Optical maps record locations of specific enzyme recognition sites within long genome fragments. This long-distance information enables aligning genome assembly contigs onto optical maps and ordering contigs into scaffolds. The ge
Externí odkaz:
https://doaj.org/article/703c2c27b1fb48eb846fd8ea00a47d3b
Autor:
John M. Urban, Michael S. Foulk, Jacob E. Bliss, C. Michelle Coleman, Nanyan Lu, Reza Mazloom, Susan J. Brown, Allan C. Spradling, Susan A. Gerbi
Publikováno v:
BMC Genomics, Vol 22, Iss 1, Pp 1-23 (2021)
Abstract Background The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisj
Externí odkaz:
https://doaj.org/article/dc3a54e02e7144beacef28bd220d2a9e
Publikováno v:
PeerJ, Vol 8, p e10150 (2020)
Motivation Long read sequencing and Bionano Genomics optical maps are two techniques that, when used together, make it possible to reconstruct entire chromosome or chromosome arms structure. However, the existing tools are often too conservative and
Externí odkaz:
https://doaj.org/article/cd7b92a3e83646e2a1219920441b1a46
Autor:
Peter A. Larsen, R. Alan Harris, Yue Liu, Shwetha C. Murali, C. Ryan Campbell, Adam D. Brown, Beth A. Sullivan, Jennifer Shelton, Susan J. Brown, Muthuswamy Raveendran, Olga Dudchenko, Ido Machol, Neva C. Durand, Muhammad S. Shamim, Erez Lieberman Aiden, Donna M. Muzny, Richard A. Gibbs, Anne D. Yoder, Jeffrey Rogers, Kim C. Worley
Publikováno v:
BMC Biology, Vol 15, Iss 1, Pp 1-17 (2017)
Abstract Background The de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome assemblies that limit downstream applications. Here, we present an iterative
Externí odkaz:
https://doaj.org/article/466164a3e1974d34be1c44854c57a46b
Autor:
Zhuozheng Shi, Fusong Ju, Shiwei Sun, Guozheng Wei, Yi Zhong, Dongbo Bu, Bin Huang, Bing Wang
Publikováno v:
BMC Bioinformatics
BMC Bioinformatics, Vol 22, Iss 1, Pp 1-17 (2021)
BMC Bioinformatics, Vol 22, Iss 1, Pp 1-17 (2021)
Background Optical maps record locations of specific enzyme recognition sites within long genome fragments. This long-distance information enables aligning genome assembly contigs onto optical maps and ordering contigs into scaffolds. The generated s
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b95010d22eda804e8374a7db178816bf
https://doi.org/10.1186/s12859-021-04448-2
https://doi.org/10.1186/s12859-021-04448-2
Autor:
Jacob E. Bliss, Susan A. Gerbi, Nanyan Lu, John M. Urban, Reza Mazloom, C Michelle Coleman, Michael S. Foulk, Susan J. Brown, Allan C. Spradling
Publikováno v:
BMC Genomics, Vol 22, Iss 1, Pp 1-23 (2021)
BMC Genomics
BMC Genomics
Background The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction d
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e9a18119d638e1fcd55b8bb37f4ccf6a
https://doi.org/10.1186/s12864-021-07926-2
https://doi.org/10.1186/s12864-021-07926-2
Publikováno v:
IEEE/ACM transactions on computational biology and bioinformatics.
A key problem in processing raw optical mapping data (Rmaps) is finding Rmaps originating from the same genomic region. These sets of related Rmaps can be used to correct errors in Rmap data, and to find overlaps between Rmaps to assemble consensus o
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::465c49e91aae4256c106af5b896a14c0
https://pubmed.ncbi.nlm.nih.gov/34057895
https://pubmed.ncbi.nlm.nih.gov/34057895
Autor:
Mélanie Massonnet, Rosa Figueroa-Balderas, Amanda M. Vondras, Dario Cantu, Noé Cochetel, Andrea Minio
Publikováno v:
G3 (Bethesda, Md.), vol 11, iss 4
G3: Genes, Genomes, Genetics, Vol 11, Iss 4 (2021)
G3: Genes|Genomes|Genetics
G3: Genes, Genomes, Genetics, Vol 11, Iss 4 (2021)
G3: Genes|Genomes|Genetics
Muscadinia rotundifolia, the muscadine grape, has been cultivated for centuries in the southeastern United States.M. rotundifoliais resistant to many of the pathogens that detrimentally affectVitis vinifera, the grape species commonly used for winema
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d1244881d1f1cc65456c7b16d80f7ed1
https://escholarship.org/uc/item/1696g82k
https://escholarship.org/uc/item/1696g82k
Publikováno v:
PeerJ, Vol 8, p e10150 (2020)
PeerJ
PeerJ
Motivation Long read sequencing and Bionano Genomics optical maps are two techniques that, when used together, make it possible to reconstruct entire chromosome or chromosome arms structure. However, the existing tools are often too conservative and
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::de451e7e04851080ac30ccec309a6d02
https://peerj.com/articles/10150.pdf
https://peerj.com/articles/10150.pdf
Publikováno v:
Journal of computational biology : a journal of computational molecular cell biology, vol 27, iss 4
RECOMB
RECOMB
Due to the current limitations of sequencing technologies,de novogenome assembly is typically carried out in two stages, namely contig (sequence) assembly and scaffolding. While scaffolding is computationally easier than sequence assembly, the scaffo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::619c00d2bf3ac3d747cc668343f6cda8
https://escholarship.org/uc/item/2mr9b7tn
https://escholarship.org/uc/item/2mr9b7tn