msa: an R package for multiple sequence alignment

Bodenhofer, Ulrich; Bonatesta, Enrico; Horejš-Kainrath, Christoph; Hochreiter, Sepp

doi:10.1093/bioinformatics/btv494

Cited by 478 publications

(347 citation statements)

References 15 publications

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“…the LCA computed with BASTA on DIAMOND results. The multiple sequence alignments were created and visualized with either the R package msa 43 or the program SeaView 44 .…”

Section: Methodsmentioning

confidence: 99%

Microbial contaminants cataloged as novel human sequences in recent human pan-genomes

Manni

Zdobnov

2020

Preprint

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Human pan-genome studies offer the opportunity to identify human non-reference sequences (NRSs) which are, by definition, not represented in the reference human genome (GRCh38). NRSs serve as useful catalogues of genetic variation for population and disease studies and while the majority consists of repetitive elements, a substantial fraction is made of non-repetitive, non-reference (NRNR) sequences. The presence of non-human sequences in these catalogues can inflate the number of "novel" human sequences, overestimate the genetic differentiation among populations, and jeopardize subsequent analyses that rely on these resources. We uncovered almost 2,000 contaminant sequences of microbial origin in NRNR sequences from recent human pan-genome studies. The contaminant contigs (3,501,302 bp) harbour genes totalling 4,720 predicted proteins (>40 aa). The major sources of contamination are related to Rhyzobiales, Burkholderiales, Pseudomonadales and Lactobacillales, which may have been associated with the original samples or introduced later during sequencing experiments. We additionally observed that the majority of human novel protein-coding genes described in one of the studies entirely overlap repetitive regions and are likely to be false positive predictions.We report here the list of contaminant sequences in three recent human pan-genome catalogues and discuss strategies to increase decontamination efficacy for current and future pan-genome studies.

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“…the LCA computed with BASTA on DIAMOND results. The multiple sequence alignments were created and visualized with either the R package msa 43 or the program SeaView 44 .…”

Section: Methodsmentioning

confidence: 99%

Microbial contaminants cataloged as novel human sequences in recent human pan-genomes

Manni

Zdobnov

2020

Preprint

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“…Using the list of retained MOTUs, the original sequence file, and the information of which sequence belongs to each MOTU (contained in the output of the clustering program used to generate MOTUs), we obtained separate MOTU files containing, for each MOTU, all sequences included with their abundances in the different samples. We then aligned sequences within each MOTU with the msa R package (Bodenhofer et al 2015), and misaligned sequences, likely due to slippage of degenerate primers (Elbrecht et al 2018b), were detected and eliminated.…”

Section: Data Setmentioning

confidence: 99%

From metabarcoding to metaphylogeography: separating the wheat from the chaff

Turon

Antich

Palacín

et al. 2019

Ecological Applications

160

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Metabarcoding is by now a well‐established method for biodiversity assessment in terrestrial, freshwater, and marine environments. Metabarcoding data sets are usually used for α‐ and β‐diversity estimates, that is, interspecies (or inter‐MOTU [molecular operational taxonomic unit]) patterns. However, the use of hypervariable metabarcoding markers may provide an enormous amount of intraspecies (intra‐MOTU) information—mostly untapped so far. The use of cytochrome oxidase (COI) amplicons is gaining momentum in metabarcoding studies targeting eukaryote richness. COI has been for a long time the marker of choice in population genetics and phylogeographic studies. Therefore, COI metabarcoding data sets may be used to study intraspecies patterns and phylogeographic features for hundreds of species simultaneously, opening a new field that we suggest to name metaphylogeography. The main challenge for the implementation of this approach is the separation of erroneous sequences from true intra‐MOTU variation. Here, we develop a cleaning protocol based on changes in entropy of the different codon positions of the COI sequence, together with co‐occurrence patterns of sequences. Using a data set of community DNA from several benthic littoral communities in the Mediterranean and Atlantic seas, we first tested by simulation on a subset of sequences a two‐step cleaning approach consisting of a denoising step followed by a minimal abundance filtering. The procedure was then applied to the whole data set. We obtained a total of 563 MOTUs that were usable for phylogeographic inference. We used semiquantitative rank data instead of read abundances to perform AMOVAs and haplotype networks. Genetic variability was mainly concentrated within samples, but with an important between seas component as well. There were intergroup differences in the amount of variability between and within communities in each sea. For two species, the results could be compared with traditional Sanger sequence data available for the same zones, giving similar patterns. Our study shows that metabarcoding data can be used to infer intra‐ and interpopulation genetic variability of many species at a time, providing a new method with great potential for basic biogeography, connectivity and dispersal studies, and for the more applied fields of conservation genetics, invasion genetics, and design of protected areas.

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“…We performed batch blastp searches of PfLCN (PF3D7_0925900) against the nr and env_nr database (Agarwala et al, 2018) using Geneious 10.2.3 (https://www.geneious.com) using an E-value of 10e-0 (BLOSUM62 substitution matrix) to identify close homologs in related apicomplexan species. A multiple sequence alignment of putative lipocalins identified in Plasmodium species was performed using MUSCLE implemented in the R package msa v1.16.0 (Bodenhofer et al, 2015).…”

Section: Identification and Evolutionary Analysis Of Lipocalin Superfmentioning

confidence: 99%

Structure-based identification and functional characterization of an essential lipocalin in the malaria parasite Plasmodium falciparum

Burda

Crosskey

Lauk

et al. 2020

Preprint

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Proteins of the lipocalin family are known to bind small hydrophobic ligands and are involved in various physiological processes ranging from lipid transport to oxidative stress responses. The genome of the malaria parasite Plasmodium falciparum contains a single protein PF3D7_0925900 with a lipocalin signature. Using crystallography and small-angle X-ray scattering, we show that the protein has a tetrameric structure of typical lipocalin monomers, hence we name it P. falciparum lipocalin (PfLCN), the first lipocalin structurally and functionally characterized in a single-celled eukaryote. We show that PfLCN is expressed in the intraerythrocytic stages of the parasite and localizes to the parasitophorous and food vacuoles. Conditional knockdown of PfLCN impairs parasite development, which can be rescued by treatment with the radical scavenger Trolox or by temporal inhibition of hemoglobin digestion. This suggests a key function of PfLCN in counteracting oxidative stress induced cell damage during multiplication of parasites within red blood cells.Keywords: blood stage / food vacuole / lipocalin / malaria / oxidative stress compound 2. Images and time-lapse movies were acquired on microscopes of the CSSB imaging facility.

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msa: an R package for multiple sequence alignment

Abstract: msa is available via the Bioconductor project: http://bioconductor.org/packages/release/bioc/html/msa.html. Further information and the R code of the example presented in this paper are available at http://www.bioinf.jku.at/software/msa/.

Cited by 478 publications

References 15 publications

Microbial contaminants cataloged as novel human sequences in recent human pan-genomes

Microbial contaminants cataloged as novel human sequences in recent human pan-genomes

From metabarcoding to metaphylogeography: separating the wheat from the chaff

Structure-based identification and functional characterization of an essential lipocalin in the malaria parasite Plasmodium falciparum

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