pfsearchV3: a code acceleration and heuristic to search PROSITE profiles

Schuepbach, Thierry; Pagni, Marco; Bridge, Alan; Bougueleret, Lydie; Xenarios, Ioannis; Cerutti, Lorenzo

doi:10.1093/bioinformatics/btt129

Cited by 21 publications

(16 citation statements)

References 8 publications

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“…The profiles were calibrated against the scrambled genome (window approach, size=60). Using pfsearchV3 (44), the assembled genome was searched for homologues matches with the DNA profile. Curated matches were extracted and aligned against each other using MAFFT (45) (version 7.305).…”

Section: Methodsmentioning

confidence: 99%

Mechanisms of surface antigenic variation in the human pathogenic fungusPneumocystis jirovecii

Schmid‐Siegert

Richard

Luraschi

et al. 2017

Preprint

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Microbial pathogens commonly escape the human immune system by varying surface proteins. We investigated the mechanisms used for that purpose by Pneumocystis jirovecii. This uncultivable fungus is an obligate pulmonary pathogen which causes pneumonia in immuno-compromised individuals, a major life-threatening infection. Long-read PacBio sequencing was used to assemble a core of subtelomeres of a single P. jirovecii strain from a bronchoalveolar lavage fluid specimen of a single patient. A total of 113 genes encoding surface proteins were identified, including 28 pseudogenes. These genes formed a subtelomeric gene superfamily which included five families encoding adhesive GPI-anchored glycoproteins, and one family encoding excreted glycoproteins. Numerical analyses suggested that diversification of the glycoproteins relies on mosaic genes created by ectopic recombination, and occurs only within each family. DNA motifs suggested that all genes are expressed independently, except those of the family encoding the most abundant surface glycoproteins which are subject to mutually exclusive expression. PCR analyses showed that exchange of the expressed gene of the latter family occurs frequently, possibly favoured by the location of the genes proximal to the telomere because this allows concomitant telomere exchange. Our observations suggest that (i) P. jirovecii cell surface is made of a complex mixture of different surface proteins, with a majority of a single isoform of the most abundant glycoprotein, (ii) genetic mosaicism within each family ensures variation of the glycoproteins, and (iii) the strategy of the fungus consists in the continuous production of new subpopulations composed of cells which are antigenically different.

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Section: Methodsmentioning

confidence: 99%

Mechanisms of surface antigenic variation in the human pathogenic fungusPneumocystis jirovecii

Schmid‐Siegert

Richard

Luraschi

et al. 2017

Preprint

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“…Residual errors in the assembly were corrected using quiver and pbalign (smrtpipe v. 2.3). ERVs in the assembled genome was annotated using a combination of alignment to known ERV sequences (Altschul, Gish, Miller, Myers, & Lipman, 1990) and by the discovery of unknown more distant family members using a profile-based approach (Schuepbach et al, 2013).…”

Section: Characterization Of the Cho Genome Ervsmentioning

confidence: 99%

Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release

Duroy

Bosshard

Schmid‐Siegert

et al. 2019

Biotech & Bioengineering

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The Chinese hamster ovary (CHO) cells used to produce biopharmaceutical proteins are known to contain type‐C endogenous retrovirus (ERV) sequences in their genome and to release retroviral‐like particles. Although evidence for their infectivity is missing, this has raised safety concerns. As the genomic origin of these particles remained unclear, we characterized type‐C ERV elements at the genome, transcriptome, and viral particle RNA levels. We identified 173 type‐C ERV sequences clustering into three functionally conserved groups. Transcripts from one type‐C ERV group were full‐length, with intact open reading frames, and cognate viral genome RNA was loaded into retroviral‐like particles, suggesting that this ERV group may produce functional viruses. CRISPR‐Cas9 genome editing was used to disrupt the gag gene of the expressed type‐C ERV group. Comparison of CRISPR‐derived mutations at the DNA and RNA level led to the identification of a single ERV as the main source of the release of RNA‐loaded viral particles. Clones bearing a Gag loss‐of‐function mutation in this ERV showed a reduction of RNA‐containing viral particle release down to detection limits, without compromising cell growth or therapeutic protein production. Overall, our study provides a strategy to mitigate potential viral particle contaminations resulting from ERVs during biopharmaceutical manufacturing.

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“…For positional annotations, the rule also needs the start and end positions of the match region on the sequence, as well as the alignment between sequence and signature. We describe this information with the EDAM and FALDO ontologies and use the alignment format returned by the pfsearchV3 [Schuepbach et al, 2013] and InterProScan [Mitchell et al, 2019] software.…”

Section: Protein Sequence/signature Matches In Rdf Syntaxmentioning

confidence: 99%

HAMAP rules as SPARQL A portable annotation pipeline for genomes and proteomes

Bolleman

Castro

Baratin

et al. 2019

Preprint

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Motivation: Genome and proteome annotation pipelines are generally custom built and therefore not easily reusable by other groups, which leads to duplication of effort, increased costs, and suboptimal results. One cost-effective way to increase the data quality in public databases is to encourage the adoption of annotation standards and technological solutions that enable the sharing of biological knowledge and tools for genome and proteome annotation.Results: We have translated the rules of our HAMAP proteome annotation pipeline to queries in the W3C standard SPARQL 1.1 syntax and applied them with two off-the-shelf SPARQL engines to UniProtKB/Swiss-Prot protein sequences described in RDF format. This approach is applicable to any genome or proteome annotation pipeline and greatly simplifies their reuse.Availability: HAMAP SPARQL rules and documentation are freely available for download from the HAMAP FTP site ftp://ftp.expasy.org/databases/hamap/hamap sparql.tar.gz under a CC-BY-ND 4.0 license. The annotations generated by the rules are under the CC-BY 4.0 license.Contact: hamap@sib.swiss Supplementary information: Supplementary data are included at the end of this document.

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pfsearchV3: a code acceleration and heuristic to search PROSITE profiles

Cited by 21 publications

References 8 publications

Mechanisms of surface antigenic variation in the human pathogenic fungusPneumocystis jirovecii

Mechanisms of surface antigenic variation in the human pathogenic fungusPneumocystis jirovecii

Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release

HAMAP rules as SPARQL A portable annotation pipeline for genomes and proteomes

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