The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
Fast-Find: A novel computational approach to analyzing combinatorial motifs
Open accessAbstract
Background: Many vital biological processes, including transcription and splicing, require a combination of short, degenerate sequence patterns, or motifs, adjacent to defined sequence features. Although these motifs occur frequently by chance, they only have biological meaning within a specific context. Identifying transcripts that contain meaningful combinations of patterns is thus an important problem, which existing tools address poorly. Results: Here we present a new approach, Fast-FIND (Fast-F ully I ndexed N ucleotide D atabase), that uses a relational database to support rapid indexed searches for arbitrary combinations of patterns defined either by sequence or composition. Fast-FIND is easy to implement, takes less than a second to search the entire Drosophila genome sequence for arbitrary patterns adjacent to sites of alternative polyadenylation, and is sufficiently fast to allow sensitivity analysis on the patterns. We have applied this approach to identify transcripts that contain combinations of sequence motifs for RNA-binding proteins that may regulate alternative polyadenylation. Conclusion: Fast-FIND provides an efficient way to identify transcripts that are potentially regulated via alternative polyadenylation. We have used it to generate hypotheses about interactions between specific polyadenylation factors, which we will test experimentally.
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Systems biology and multi-omics integration: viewpoints from the metabolomics research community
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TSEBRA: transcript selector for BRAKER
Gabriel, L., Hoff, K. J., Brůna, T., Borodovsky, M., & Stanke, M. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04482-0 · Cited by 410
Topic modeling for untargeted substructure exploration in metabolomics
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Cracking the black box of deep sequence-based protein–protein interaction prediction
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Metadata
- Authors
- Hamady, M., Peden, E., Knight, R., & Singh, R.
- Venue
- BMC Bioinformatics
- Published
- 2006-01-04
- Volume
- 7
- Issue
- 1
- Pages
- 1-1
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W1504401263
- Cited by
- 543
- References
- 38
- FWCI
- 3.32
- Type
- journal article
- Language
- en
- Open access
- gold
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