Using Galaxy to Perform Large‐Scale Interactive Data Analyses—An Update

Ostrovsky, Alexander; Hillman-Jackson, Jennifer; Bouvier, Dave; Clements, D. L.; Afgan, Enis; Blankenberg, Daniel; Schatz, Michael C.; Nekrutenko, Anton; Taylor, James; Larivière, Delphine

doi:10.1002/cpz1.31

Cited by 7 publications

(3 citation statements)

References 22 publications

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“…The database contains 28.513 RE and is made of “RepeatMasker” hits for 60 HERV families (RepeatMasker Open-4.0, http://www.repeatmasker.org/ ) and all LINE elements from “L1base v2” ( https://l1base.charite.de/ ) [ 83 ]. Alignment of the retro.hg38.v1 database to CoV genomes was done by the genome sequence aligner “nucmer” [ 84 ] (4.0.0beta2) on galaxy.org [ 85 ] and a local installation of “LAST” (v1250), a programme for genome scale sequence comparison [ 86 ]. The minimum sequence length cut-off (with 100% sequence identity) was stepwise chosen at 12, 15, 18, 21, 24, and ≥ 27, based on an immuno-relevant epitope size of about 4 – 12 amino acids (aa) (many epitopes are less than 8 aa, about 25% ≤ 6 aa, but only a few at 4 aa [ 51 ]).…”

Section: Methodsmentioning

confidence: 99%

SARS-CoV-2 and human retroelements: a case for molecular mimicry?

Koch

2022

BMC Genom Data

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Background The factors driving the late phase of COVID-19 are still poorly understood. However, autoimmunity is an evolving theme in COVID-19’s pathogenesis. Additionally, deregulation of human retroelements (RE) is found in many viral infections, and has also been reported in COVID-19. Results Unexpectedly, coronaviruses (CoV) – including SARS-CoV-2 – harbour many RE-identical sequences (up to 35 base pairs), and some of these sequences are part of SARS-CoV-2 epitopes associated to COVID-19 severity. Furthermore, RE are expressed in healthy controls and human cells and become deregulated after SARS-CoV-2 infection, showing mainly changes in long interspersed nuclear element (LINE1) expression, but also in endogenous retroviruses. Conclusion CoV and human RE share coding sequences, which are targeted by antibodies in COVID-19 and thus could induce an autoimmune loop by molecular mimicry.

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Section: Methodsmentioning

confidence: 99%

SARS-CoV-2 and human retroelements: a case for molecular mimicry?

Koch

2022

BMC Genom Data

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“…We first PLOS ONE generated a P. falciparum W2 strain variant-corrected genome index for read alignment as this strain was used for ribo-seq. Whole genome sequence (WGS) data of the P. falciparum W2 strain reported in [10] under SRA accession number SRR1335983 were analyzed using tools hosted by the public server at usegalaxy.org [103]. The WGS data were pre-processed using the Trimmomatic tool, aligned to the P. falciparum 3D7 v3.2 reference genome and variants called following the recommendations for haploid genomes [104].…”

Section: Analysis Of Protein Coding Function From Ribosome Profilingmentioning

confidence: 99%

Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing

et al. 2022

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The Plasmodium falciparum human malaria parasite genome is incompletely annotated and does not accurately represent the transcriptomic diversity of this species. To address this need, we performed long-read transcriptomic sequencing. 5′ capped mRNA was enriched from samples of total and nuclear-fractionated RNA from intra-erythrocytic stages and converted to cDNA library. The cDNA libraries were sequenced on PacBio and Nanopore long-read platforms. 12,495 novel isoforms were annotated from the data. Alternative 5′ and 3′ ends represent the majority of isoform events among the novel isoforms, with retained introns being the next most common event. The majority of alternative 5′ ends correspond to genomic regions with features similar to those of the reference transcript 5′ ends. However, a minority of alternative 5′ ends showed markedly different features, including locations within protein-coding regions. Alternative 3′ ends showed similar features to the reference transcript 3′ ends, notably adenine-rich termination signals. Distinguishing features of retained introns could not be observed, except for a tendency towards shorter length and greater GC content compared with spliced introns. Expression of antisense and retained intron isoforms was detected at different intra-erythrocytic stages, suggesting developmental regulation of these isoform events. To gain insights into the possible functions of the novel isoforms, their protein-coding potential was assessed. Variants of P. falciparum proteins and novel proteins encoded by alternative open reading frames suggest that P. falciparum has a greater proteomic repertoire than the current annotation. We provide a catalog of annotated transcripts and encoded alternative proteins to support further studies on gene and protein regulation of this pathogen.

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“…With this in mind, many integrated computational tools were developed to help researchers with no particular informatic skills to work on their data. The most emblematic is the Galaxy web platform [12], which is based on a tool shed gathering several thousand software packages. Clearly, technical resources exist today, as well as training programs to learn how to use them [13].…”

Section: Introductionmentioning

confidence: 99%

Omics Analyses: How to Navigate Through a Constant Data Deluge

Denecker

Lelandais

2022

Methods in Molecular Biology

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Omics data are very valuable for researchers in biology, but the work required to develop a solid expertise in their analysis contrasts with the rapidity with which the omics technologies evolve. Data accumulate in public databases, and despite significant advances in bioinformatics softwares to integrate them, data analysis remains a burden for those who perform experiments. Beyond the issue of dealing with a very large number of results, we believe that working with omics data requires a change in the way scientific problems are solved. In this chapter, we explain pitfalls and tips we found during our functional genomics projects in yeasts. Our main lesson is that, if applying a protocol does not guarantee a successful project, following simple rules can help to become strategic and intentional, thus avoiding an endless drift into an ocean of possibilities.

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Using Galaxy to Perform Large‐Scale Interactive Data Analyses—An Update

Cited by 7 publications

References 22 publications

SARS-CoV-2 and human retroelements: a case for molecular mimicry?

SARS-CoV-2 and human retroelements: a case for molecular mimicry?

Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing

Omics Analyses: How to Navigate Through a Constant Data Deluge

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