Zobrazeno 1 - 10
of 15
pro vyhledávání: '"Chengze Shen"'
Publikováno v:
Algorithms for Molecular Biology, Vol 18, Iss 1, Pp 1-14 (2023)
Abstract Background Adding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with new data, adding sequences into a constraint alignment constructed using biological knowledg
Externí odkaz:
https://doaj.org/article/3ff599092538409eb4e3b3b0db256f89
Publikováno v:
Scientific Reports, Vol 13, Iss 1, Pp 1-11 (2023)
Abstract Finding alignments between millions of reads and genome sequences is crucial in computational biology. Since the standard alignment algorithm has a large computational cost, heuristics have been developed to speed up this task. Though orders
Externí odkaz:
https://doaj.org/article/5c3408cd12bf4298a946409433ace604
Publikováno v:
Bioinformatics
Summary Multiple sequence alignment is an initial step in many bioinformatics pipelines, including phylogeny estimation, protein structure prediction and taxonomic identification of reads produced in amplicon or metagenomic datasets, etc. Yet, alignm
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f5f0bd806b2e9da4584e91586a63a2c3
https://doi.org/10.1093/bioinformatics/btab788
https://doi.org/10.1093/bioinformatics/btab788
Phylogenetic placement, the problem of placing sequences into phylogenetic trees, has been limited either by the number of sequences placed in a single run or by the size of the placement tree. The most accurate scalable phylogenetic placement method
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e070582119282ef6dbf2a08d48ac4305
https://doi.org/10.1101/2022.10.26.513936
https://doi.org/10.1101/2022.10.26.513936
Multiple sequence alignment is essential for many biological downstream analyses, but accurate alignment of large datasets, especially those exhibiting high rates of evolution or sequence length heterogeneity, is still unsolved. We present SALMA, a n
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::5c9dfb824cd1b7316a14c1c7c6bf0166
https://doi.org/10.1101/2022.05.23.493139
https://doi.org/10.1101/2022.05.23.493139
WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model Alignment
Publikováno v:
Journal of computational biology : a journal of computational molecular cell biology. 29(8)
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6a0f4aebf29279f41cf021202e22026d
https://pubmed.ncbi.nlm.nih.gov/35575747
https://pubmed.ncbi.nlm.nih.gov/35575747
MotivationMultiple sequence alignment (MSA) is a basic step in many bioinformatics pipelines. However, achieving highly accurate alignments on large datasets, especially those with sequence length heterogeneity, is a challenging task. UPP (Ultra-larg
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b37e537538f3e9f087bbefcb658d3c3f
https://doi.org/10.1101/2022.02.26.482099
https://doi.org/10.1101/2022.02.26.482099
Autor:
Shen, Chengze1 (AUTHOR), Liu, Baqiao1 (AUTHOR), Williams, Kelly P.2 (AUTHOR), Warnow, Tandy1 (AUTHOR) warnow@illinois.edu
Publikováno v:
Algorithms for Molecular Biology. 12/7/2023, Vol. 18 Issue 1, p1-14. 14p.
Autor:
Mongia, Mihir1 (AUTHOR), Shen, Chengze1,2 (AUTHOR), Davoodi, Arash Gholami1,3 (AUTHOR), Marçais, Guillaume1 (AUTHOR), Mohimani, Hosein1 (AUTHOR) hoseinm@cs.cmu.edu
Publikováno v:
Scientific Reports. 5/4/2023, Vol. 13 Issue 1, p1-11. 11p.
Publikováno v:
Journal of Computational Biology; Aug2022, Vol. 29 Issue 8, p782-801, 20p