Logomaker: Beautiful sequence logos in python

Tareen, Ammar; Kinney, Justin B.

doi:10.1101/635029

Cited by 36 publications

(23 citation statements)

References 17 publications

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“…The letter heights were then computed by re-scaling the weighting factors at each site to sum to one, so that the letter height is pr,a = wr,a / ∑a' wr,a'. The logo plots themselves were rendered using Logomaker (Tareen and Kinney, 2020). The code that creates these logo plots is on GitHub at https://github.com/jbloomlab/SARS-CoV-2-RBD_DMS/blob/master/results/summary/logoplots_of_muteffects.md.…”

Section: Data Visualizationmentioning

confidence: 99%

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

Starr

Greaney

Hilton

et al. 2020

Preprint

615

1,193

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The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor, and is a major determinant of host range and a dominant target of neutralizing antibodies. Here we experimentally measure how all amino-acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD's surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance.

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Section: Data Visualizationmentioning

confidence: 99%

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

Starr

Greaney

Hilton

et al. 2020

Preprint

615

1,193

View full text Add to dashboard Cite

show abstract

“…Wu & Bartel, 2017) to test whether a given nucleotide at each position increased or decreased the likelihood of stimulating SCR. P values were adjusted using the Benjamini-Hochberg procedure (Benjamini & Hochberg, 1995) and plotted using Logomaker (Tareen & Kinney, 2019) for untreated (top) and G418-treated (bottom) cells ( Figure 5A and blow up of G418 data in Figure 5 -figure supplement 1A). As an alternative approach, we used a linear regression model to calculate regression coefficients for every nucleotide in the sequence window ( Figure 5 -figure supplement 1B), a strategy that has been previously applied to readthrough of luciferase reporters (Schueren et al, 2014).…”

Section: Stop Codon Identity and Mrna Context Influence Probability Omentioning

confidence: 99%

Stop Codon Context Influences Genome-Wide Stimulation of Termination Codon Readthrough by Aminoglycosides

Wangen

Green

2019

Preprint

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Stop codon readthrough (SCR) occurs when the ribosome miscodes at a stop codon. Such readthrough events can be therapeutically desirable when a premature termination codon (PTC) is found in a critical gene. To study SCR in vivo in a genome-wide manner, we treated mammalian cells with aminoglycosides and performed ribosome profiling. We find that in addition to stimulating readthrough of PTCs, aminoglycosides stimulate readthrough of normal termination codons (NTCs) genome-wide. Stop codon identity, the nucleotide following the stop codon, and the surrounding mRNA sequence context all influence the likelihood of SCR. In comparison to NTCs, downstream stop codons in 3′UTRs are recognized less efficiently by ribosomes, suggesting that targeting of critical stop codons for readthrough may be achievable without general disruption of translation termination. Finally, we find that G418 treatment globally alters gene expression with substantial effects on translation of histone genes, selenoprotein genes, and S-adenosylmethionine decarboxylase (AMD1).

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“…Substitution matrix was BLOSUM62 and the gap penalty was set to 10. Sequence logos were produced using logomaker module for Python (Tareen and Kinney, 2019).…”

Section: Multiple Sequence Alignmentmentioning

confidence: 99%

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

Midlik

Navrátilová

Moturu

et al. 2020

Preprint

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Motivation:Protein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of homologous structures and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, assigning always the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs and their variability provides an overview of the studied protein family and can be used to enrich the analysis of a particular protein at hand. Results: We developed a workflow for analysis of the secondary structure anatomy of a protein family, based on SSE annotation tool SecStrAnnotator. We applied this analysis to the model family of cytochromes P450 (CYPs)a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, as well as the conservation/variability of these properties. We also suggest a generic residue numbering scheme for the CYP family. The comparison between the bacterial and eukaryotic part of the family highlights the major differences and reveals an anomalous group of bacterial CYPs with some typically eukaryotic features. This hints at possible evolutionary and functional relationships.

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Logomaker: Beautiful sequence logos in python

Cited by 36 publications

References 17 publications

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

Stop Codon Context Influences Genome-Wide Stimulation of Termination Codon Readthrough by Aminoglycosides

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

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