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SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets
Open accessPreprint — published as 10.1093/bioinformatics/btad488
Abstract
The emergence of high-throughput experiments and high-resolution computational predictions has led to an explosion in the quality and volume of protein sequence annotations at proteomic scales. Unfortunately, integrating and analyzing complex sequence annotations remains logistically challenging. Here we present SHEPHARD, a software package that makes large-scale integrative protein bioinformatics trivial. SHEPHARD is provided as a stand-alone package and with a pre-compiled set of human annotations in a Google Colab notebook.
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Metadata
- Authors
- Ginell, G. M., Flynn, A. J., & Holehouse, A. S.
- Affiliations
- Washington University in St. Louis (US)
- Corresponding author
- Holehouse, Alex S.
- Venue
- Bioinformatics
- Publisher
- openRxiv
- Published
- 2022-09-19
- Volume
- 39
- Issue
- 8
- ISSN
- 1367-4803 (ISSN-L)
- PMC
- PMC10423030
- OpenAlex
- W4385564401
- Cited by
- 8
- References
- 1
- Citations by year
- 2025: 2 · 2024: 4 · 2023: 2
- FWCI
- 0.71
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Commons@Becker (Washington University School of Medicine) (submittedVersion, cc-by)
- Funders
- National Science Foundation (2213983, 2128068)
- Longer Life Foundation
- Division of Biological Infrastructure (2213983)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Keywords
- protein sequence annotation, proteomics, integrative bioinformatics, software architecture, Python framework, hierarchical data structures, annotation integration, proteome-wide analysis
- MeSH terms
- Software, Computational Biology, Proteome, Proteomics, Molecular Sequence Annotation
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