Logomaker: beautiful sequence logos in Python

Tareen, Ammar; Kinney, Justin B.

doi:10.1093/bioinformatics/btz921

Cited by 342 publications

(301 citation statements)

References 36 publications

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“…Analysis(MEGA)(44) using the Maximum Likelihood method. The sequence logo was plotted from aligned sequences by logomaker (45).…”

Section: Contributionsmentioning

confidence: 99%

Versatile, Multivalent Nanobody Cocktails Efficiently Neutralize SARS-CoV-2

Xiang

Nambulli

Xiao

et al. 2020

Preprint

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The outbreak of COVID-19 has severely impacted global health and economy. Cost-effective therapeutics are urgently needed. Here, we used camelid immunization and proteomics to identify a large repertoire of highly potent neutralizing nanobodies (Nbs) to the SARS-CoV-2 spike protein receptor-binding domain (RBD). We discovered multiple elite Nbs of picomolar to femtomolar affinities that inhibit viral infection at as low as sub-ng/ml concentration, more potent than some of the best human neutralizing antibodies. We then determined a crystal structure of such an elite neutralizing Nb in complex with RBD. Structural proteomics and integrative modeling revealed multiple distinct and non-overlapping epitopes and indicated an array of potential neutralization mechanisms. Structural characterization facilitated the bioengineering of novel multivalent Nb constructs into multi-epitope cocktails that achieved ultrahigh neutralization potency (IC50s as low as 0.058 ng/ml) and may prevent mutational escape. Our Nbs can be rapidly produced in bulk from microbes and resist heat, lyophilization, and aerosolization. These highly promising agents are readily translated into efficient, economic, and convenient therapeutics to help end this once-in-a-century health crisis.

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“…Analysis(MEGA)(44) using the Maximum Likelihood method. The sequence logo was plotted from aligned sequences by logomaker (45).…”

Section: Contributionsmentioning

confidence: 99%

Versatile, Multivalent Nanobody Cocktails Efficiently Neutralize SARS-CoV-2

Xiang

Nambulli

Xiao

et al. 2020

Preprint

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“…The tree is provided in Supplementary Figure 59 . The logo for the catalytic site was generated with logomaker v0.8 in python v2.7.15 106 .…”

Section: Methodsmentioning

confidence: 99%

Undinarchaeota illuminate the evolution of DPANN archaea

Dombrowski

Williams

Sun

et al. 2020

Preprint

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14 15 #corresponding author. Postal address: Landsdiep 4, 1797 SZ 't Horntje (Texel). Email address: anja.spang@nioz.nl. Phone16 number: +31 (0)222 369 526 17 18 19Several recent studies have revealed the presence of a thus far uncharacterized archaeal lineage 77 referred to the Uncultivated Archaeal Phylum 2 (UAP2) 13,40,41 , which seems to affiliate with DPANN 78 archaea and thus may be key in resolving long-standing debates regarding archaeal phylogeny and the 79 evolution of DPANN. In this study, we have used a metagenomics approach to obtain additional genomes 80 of members of the so far uncharacterized UAP2 and provide first insights into their metabolic repertoire 81 and lifestyle. Furthermore, we implemented comprehensive and careful phylogenomic techniques aimed 82 at ameliorating phylogenetic artifacts, shedding new light onto the evolutionary origin and phylogenetic 83 placement of the various DPANN lineages including UAP2 in an updated archaeal phylogeny. 84 Results and Discussion 85A thus far uncharacterized putative archaeal phylum-level lineage in metagenome read archives 86The generation of a large diversity of metagenome-assembled genomes (MAGs) representing 87 archaeal and bacterial lineages across the tree of life has led to the definition of the tentative archaeal 88 UAP2 phylum 41 . Considering our lack of insights into the biology of members of this lineage as well as its 89suggested key position in the archaeal tree, we aimed at obtaining a broader genomic representation of 90 the UAP2. In particular, we screened publicly available metagenomes using ribosomal protein sequences 91 of the previously reconstructed UAP2 MAGs and assembled and binned UAP2-positive samples yielding 92 six additional MAGs belonging to the UAP2 lineage (Table 1, Supplementary Tables 1-2, see Methods for 93 details). Four of the newly assembled MAGs were recovered from metagenomes of a groundwater aquifer 94 located adjacent to the Colorado River 42 , while the two others as well as six previously reconstructed 95MAGs, derived from metagenomes of marine waters in the Atlantic 41,43 and Indian Oceans 44 as well as the 96Mediterranean Sea 45 (Supplementary Table 2). UAP2 representatives were detected in samples from 97 various depths in the water column (85-5000 m), fluctuating oxygen conditions (anoxic to oxic) and 98 temperatures (sampling sites had temperatures from 18 up to 106°C) (Supplementary Figure 1, 99

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“…To test whether published RIN motifs are enriched in genes co-immunoprecipitated with RIN in our analysis, we used in vitro-determined Drosophila RIN and human G3BP2 motifs (Cook et al, 2011;Ray et al, 2013) (see http://cisbp-rna.ccbr.utoronto.ca/), and in vivo motifs of human G3BP1 and G3BP2 (Edupuganti et al, 2017). Position frequency matrices (PFMs) of the in vivo motifs were estimated from the height of base logos and produced using ggseqlogo (Wagih, 2017) and Logomaker (Tareen and Kinney, 2019). To eliminate the effect of sequence length on motif enrichment, we randomly selected corresponding transcript regions from length-paired co-expressed unbound genes as negative set for each transcript region of genes in the RIP-enriched gene sets (positive set).…”

Section: Enrichment Test Of Published Rin Motifsmentioning

confidence: 99%