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Popset specifications

Information


Unique identifier OMICS_14036
Name Popset
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Eric W Sayers

Publication for Popset

Popset citations

 (21)
library_books

Photobiont switching causes changes in the reproduction strategy and phenotypic dimorphism in the Arthoniomycetes

2018
Sci Rep
PMCID: 5862901
PMID: 29563606
DOI: 10.1038/s41598-018-23219-3

[…] In case of algal nuITS rDNA region, the newly obtained sequences were aligned together with Trebouxia sequences generated in the study of Voytsekhovich & Beck which are deposited in GenBank as PopSet 940816236 and additionally with best-hits from BLAST searches of newly sequenced photobionts, i.e. Trebouxia sp. TR9 (KU716051) and Trebouxia sp. P-400-IaSc (AM159210), using MAFFT on XSEDE (7. […]

library_books

Classification of infectious bursal disease virus into genogroups

2017
Arch Virol
PMCID: 5671532
PMID: 28825213
DOI: 10.1007/s00705-017-3500-4

[…] Cycle sequencing was conducted at the University of Wisconsin Biotechnology Center DNA Sequencing Facility (Madison, WI). DNA sequences were submitted to GenBank (accession numbers MF142502-MF142591, PopSet 1229404744 for VP2 and MF142461-MF142501, PopSet 1229404662 for VP1). Nucleotide and predicted amino acid sequences were aligned with those of reference strains from GenBank (Table ) using Gene […]

library_books

Association mapping of starch chain length distribution and amylose content in pea (Pisum sativum L.) using carbohydrate metabolism candidate genes

2017
BMC Plant Biol
PMCID: 5540500
PMID: 28764648
DOI: 10.1186/s12870-017-1080-9

[…] likelihood that a variant might have an effect on protein biological function was carried out using the Protein Variant Effect Analyzer (PROVEAN) ver. 1.1 []. Sequences are lodged as population set (PopSet) alignments (Table ) with GenBank (sequences KM360195-KM360301, KM510517-KM513542 and KY983278-KY983354). […]

call_split

Molecular characterization reveals the complexity of previously overlooked coral exosymbiont interactions and the implications for coral guild ecology

2017
Sci Rep
PMCID: 5372162
PMID: 28358026
DOI: 10.1038/srep44923
call_split See protocol

[…] a and Alpheus, as well as outgroup sequences, and these were added to previous alignments. For the hosts, the ORF sequences were aligned with those generated by Schmidt-Roach et al. as the reference (PopSet accession number: 413910611). […]

library_books

What causes mating system shifts in plants? Arabidopsis lyrata as a case study

2016
Heredity
PMCID: 5176122
PMID: 27804968
DOI: 10.1038/hdy.2016.99

[…] x domain protein; At4g21350) and B70 (Ethylene-responsive protein-like transcription factor; At4g21340) are downstream. For all individuals in our study, B80 and B160 had been sequenced previously (; Popset accessions: 374282218 and 374282986); here we used primers developed by to sequence and genotype B70 and B120. Strategies for direct sequencing, cloning and haplotype resolution were as descri […]

library_books

18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species

2016
Ecol Evol
PMCID: 4801955
PMID: 27087935
DOI: 10.1002/ece3.1986

[…] es were combined with forty‐eight individual 18S V9 sequences including 12 copepod and eight euphausiid species inhabiting North East Atlantic (NEA) waters (respectively, Laakmann et al. and GenBank popset 117414780; Table S2). The sequences were aligned using MUSCLE (Edgar ) implemented in MEGA5 (Tamura et al. ). Based on the resulting multiple sequence alignment (MSA), a maximum likelihood (ML) […]

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Popset institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

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