ScanFold 2.0: a rapid approach for identifying potential structured RNA targets in genomes and transcriptomes
A major limiting factor in target discovery for both basic research and therapeutic intervention is the identification of structural and/or functional RNA elements in genomes and transcriptomes. This was the impetus for the original ScanFold algorithm, which provides maps of local RNA structural sta...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2022-11-01
|
| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/14361.pdf |
| _version_ | 1797421064765046784 |
|---|---|
| author | Ryan J. Andrews Warren B. Rouse Collin A. O’Leary Nicholas J. Booher Walter N. Moss |
| author_facet | Ryan J. Andrews Warren B. Rouse Collin A. O’Leary Nicholas J. Booher Walter N. Moss |
| author_sort | Ryan J. Andrews |
| collection | DOAJ |
| description | A major limiting factor in target discovery for both basic research and therapeutic intervention is the identification of structural and/or functional RNA elements in genomes and transcriptomes. This was the impetus for the original ScanFold algorithm, which provides maps of local RNA structural stability, evidence of sequence-ordered (potentially evolved) structure, and unique model structures comprised of recurring base pairs with the greatest structural bias. A key step in quantifying this propensity for ordered structure is the prediction of secondary structural stability for randomized sequences which, in the original implementation of ScanFold, is explicitly evaluated. This slow process has limited the rapid identification of ordered structures in large genomes/transcriptomes, which we seek to overcome in this current work introducing ScanFold 2.0. In this revised version of ScanFold, we no longer explicitly evaluate randomized sequence folding energy, but rather estimate it using a machine learning approach. For high randomization numbers, this can increase prediction speeds over 100-fold compared to ScanFold 1.0, allowing for the analysis of large sequences, as well as the use of additional folding algorithms that may be computationally expensive. In the testing of ScanFold 2.0, we re-evaluate the Zika, HIV, and SARS-CoV-2 genomes and compare both the consistency of results and the time of each run to ScanFold 1.0. We also re-evaluate the SARS-CoV-2 genome to assess the quality of ScanFold 2.0 predictions vs several biochemical structure probing datasets and compare the results to those of the original ScanFold program. |
| first_indexed | 2024-03-09T07:11:32Z |
| format | Article |
| id | doaj.art-974e03753a5b44e8ab290d91009c1eca |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:11:32Z |
| publishDate | 2022-11-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-974e03753a5b44e8ab290d91009c1eca2023-12-03T09:06:46ZengPeerJ Inc.PeerJ2167-83592022-11-0110e1436110.7717/peerj.14361ScanFold 2.0: a rapid approach for identifying potential structured RNA targets in genomes and transcriptomesRyan J. Andrews0Warren B. Rouse1Collin A. O’Leary2Nicholas J. Booher3Walter N. Moss4Department of Biochemistry, University of Utah, Salt Lake City, UT, United StatesThe Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United StatesThe Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United StatesInfrastructure and Research IT Services, Iowa State University, Ames, IA, United StatesThe Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United StatesA major limiting factor in target discovery for both basic research and therapeutic intervention is the identification of structural and/or functional RNA elements in genomes and transcriptomes. This was the impetus for the original ScanFold algorithm, which provides maps of local RNA structural stability, evidence of sequence-ordered (potentially evolved) structure, and unique model structures comprised of recurring base pairs with the greatest structural bias. A key step in quantifying this propensity for ordered structure is the prediction of secondary structural stability for randomized sequences which, in the original implementation of ScanFold, is explicitly evaluated. This slow process has limited the rapid identification of ordered structures in large genomes/transcriptomes, which we seek to overcome in this current work introducing ScanFold 2.0. In this revised version of ScanFold, we no longer explicitly evaluate randomized sequence folding energy, but rather estimate it using a machine learning approach. For high randomization numbers, this can increase prediction speeds over 100-fold compared to ScanFold 1.0, allowing for the analysis of large sequences, as well as the use of additional folding algorithms that may be computationally expensive. In the testing of ScanFold 2.0, we re-evaluate the Zika, HIV, and SARS-CoV-2 genomes and compare both the consistency of results and the time of each run to ScanFold 1.0. We also re-evaluate the SARS-CoV-2 genome to assess the quality of ScanFold 2.0 predictions vs several biochemical structure probing datasets and compare the results to those of the original ScanFold program.https://peerj.com/articles/14361.pdfRNAMotif discoveryRNA structureGenome annotationSequence analysis |
| spellingShingle | Ryan J. Andrews Warren B. Rouse Collin A. O’Leary Nicholas J. Booher Walter N. Moss ScanFold 2.0: a rapid approach for identifying potential structured RNA targets in genomes and transcriptomes PeerJ RNA Motif discovery RNA structure Genome annotation Sequence analysis |
| title | ScanFold 2.0: a rapid approach for identifying potential structured RNA targets in genomes and transcriptomes |
| title_full | ScanFold 2.0: a rapid approach for identifying potential structured RNA targets in genomes and transcriptomes |
| title_fullStr | ScanFold 2.0: a rapid approach for identifying potential structured RNA targets in genomes and transcriptomes |
| title_full_unstemmed | ScanFold 2.0: a rapid approach for identifying potential structured RNA targets in genomes and transcriptomes |
| title_short | ScanFold 2.0: a rapid approach for identifying potential structured RNA targets in genomes and transcriptomes |
| title_sort | scanfold 2 0 a rapid approach for identifying potential structured rna targets in genomes and transcriptomes |
| topic | RNA Motif discovery RNA structure Genome annotation Sequence analysis |
| url | https://peerj.com/articles/14361.pdf |
| work_keys_str_mv | AT ryanjandrews scanfold20arapidapproachforidentifyingpotentialstructuredrnatargetsingenomesandtranscriptomes AT warrenbrouse scanfold20arapidapproachforidentifyingpotentialstructuredrnatargetsingenomesandtranscriptomes AT collinaoleary scanfold20arapidapproachforidentifyingpotentialstructuredrnatargetsingenomesandtranscriptomes AT nicholasjbooher scanfold20arapidapproachforidentifyingpotentialstructuredrnatargetsingenomesandtranscriptomes AT walternmoss scanfold20arapidapproachforidentifyingpotentialstructuredrnatargetsingenomesandtranscriptomes |