Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files

Roberson, Elisha D.O.

doi:10.1093/bioinformatics/bty437

Cited by 9 publications

(5 citation statements)

References 29 publications

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“…I calculated the GC content of each genome using a Python script with the pyfaidx package (v0.5.5.2) [8]. I then identified the potential CasX editing sites in each genome using Motif Scraper (v1.0.2) with the motif TTCNNNNNNNNNNNNNNNNNNNNN and multiple cores in file buffered mode [9]. The standard Motif Scraper options buffer all sites in memory for sorting later based on the order of contigs in the input FASTA file.…”

Section: Construction and Contentmentioning

confidence: 99%

A catalog of CasX genome editing sites in common model organisms

Roberson

2019

BMC Genomics

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DpbCasX, also called Cas12e, is an RNA-guided DNA endonuclease isolated from Deltaproteobacteria . In this paper I characterized the CasX-compatible genome editing sites in the reference genomes of yeast ( Saccharomyces cerevisiae) , flatworms ( Caenorhabditis elegans) , flies ( Drosophila melanogaster ), zebrafish ( Danio rerio ), mouse ( Mus musculus ), rats ( Rattus norvegicus ), and humans ( Homo sapiens ). Across those genomes there were > 27,000 CasX sites per megabase on average. More than 90% of genes in each genome had at least one unique site overlapping an exon, with median unique sites per gene of 6–45. I also annotated sites in the GRCm38 reference and 15 additional mouse strain genomes. The presence of specific guide sequences varied amongst the strains, with CAST/EiJ and PWK/PhJ showing the greatest divergence from the reference strain. The high density of CasX sites and number of exon overlapping sites suggests that CasX has the potential to be used as a common genome editor. Electronic supplementary material The online version of this article (10.1186/s12864-019-5924-6) contains supplementary material, which is available to authorized users.

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Section: Construction and Contentmentioning

confidence: 99%

A catalog of CasX genome editing sites in common model organisms

Roberson

2019

BMC Genomics

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“…I calculated the GC content of each genome using a Python script with the pyfaidx package (v0.5.5.2) (Shirley et al 2015). I then identified the potential CasX editing sites in each genome using Motif Scraper (v1.0.2) with the motif TTCNNNNNNNNNNNNNNNNNNNNN and multiple cores in file buffered mode (Roberson 2018). The standard Motif Scraper options buffer all sites in memory for sorting later based on the order of contigs in the input FASTA file.…”

Section: Identification Of Casx Sitesmentioning

confidence: 99%

A catalog of CasX genome editing sites in common model organisms

Roberson

2019

Preprint

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DpbCasX, also called Cas12e, is an RNA-guided DNA endonuclease isolated from Deltaproteobacteria. In this paper I characterized the CasX-compatible genome editing sites in the reference genomes of yeast (Saccharomyces cerevisiae), flatworms (Caenorhabditis elegans), flies (Drosophila melanogaster), zebrafish (Danio rerio), mouse (Mus musculus), rats (Rattus norvegicus), and humans (Homo sapiens). Across those genomes there were >27,000 CasX sites per megabase on average. More than 90% of genes in each genome had at least one unique site overlapping an exon, with median unique sites per gene of 6 -45. I also annotated sites in the GRCm38 reference and 15 additional mouse strain genomes. The presence of specific guide sequences varied amongst the strains, with CAST/EiJ and PWK/PhJ showing the greatest divergence from the reference strain.The high density of CasX sites and number of exon overlapping sites suggests that CasX has the potential to be used as a common genome editor.

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“…Typically, motifs conform to a particular sequence pattern, where certain positions can be constrained to a specific amino acid, whereas others are not [27]. This confers a high degeneration of the motifs yielding a huge list of non-redundant motif sequences and consequently, some motifs that are not characteristics of effector sequences only [28]. Furthermore, different amino acids (AAs) can have similar physicochemical properties, thus different motif sequences can share similar properties.…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of specific motifs in effector proteins of plant parasites using MOnSTER

Calia,

Porracciolo,

Chen

et al. 2023

Preprint

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Plant pathogens cause billions of dollars of crop loss every year and are a major threat to global food security. Identifying and characterizing pathogens effectors is crucial towards their improved control. Because of their poor sequence conservation, effector identification in protein sequences predicted from genomes is challenging and current methods generate too many candidates without indication for prioritizing further experimental studies. In most phyla, effectors contain specific sequence motifs which influence their localization and targets in the plant. Although bacterial, fungal and oomycetes effectors have been studied extensively and conserved characteristic motifs have been identified, research on plant-parasitic nematode effectors (PPN) identified some enriched degenerate motifs in only one species so far. The different lifestyles of PPNs might reflect effectors with different functions according to the nematode's specific needs, thus presenting a high variety of characteristic motifs. To circumvent these limitations, we have developed MOnSTER a novel tool that identifies clusters of motifs of protein sequences (CLUMP) and associates a score to each CLUMP. This score encompasses the physicochemical properties of AAs and the motif occurrences. We built up our method to identify discriminant CLUMPs in effector proteins of plant-pathogenic oomycetes. We showed the reliability of MOnSTER by identifying five CLUMPs that correspond to the known motifs: RxLR, -dEER and LxLFLAK-HVLVxxP. Consequently, we applied MOnSTER on PPN effector proteins and identified peculiar motifs in their sequences. We identified six CLUMPs in about 60% of the known nematode effectors. Furthermore, we found that specific co-occurrences of at least two CLUMPs are present in PPN effector sequences bearing protein domains important for invasion and pathogenicity. The potentiality of this tool goes behind the effector proteins and can be used to easily cluster motifs and calculate the CLUMPs score on any set of protein sequences.

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Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files

Abstract: The motif scraper package (MIT license) is available via PyPI, and the Python source is available on GitHub at https://github.com/RobersonLab/motif_scraper.

Cited by 9 publications

References 29 publications

A catalog of CasX genome editing sites in common model organisms

A catalog of CasX genome editing sites in common model organisms

A catalog of CasX genome editing sites in common model organisms

Identification and characterization of specific motifs in effector proteins of plant parasites using MOnSTER

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