InterPro and InterProScan: tools for protein sequence classification and comparison.
By Nicola J. Mulder, Rolf Apweiler. Methods in molecular biology, 2007
322 citations recorded by the source corpus.
Subfields: Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/20e6312705a8716eccdd467e83d28b33e4f25d8b
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In Molecular Biology
- Anushya Muruganujan
- Huaiyu Mi
- Paul D. Thomas
- Dan Ofer
- Michal Linial
- Björn Usadel
- G. Ponce-Soto
- K. Krause
In Spectroscopy
- Huaiyu Mi
- Paul D. Thomas
- Mark Yandell
- Daniel Ence
- Anushya Muruganujan
- Mark Stitt
- Björn Usadel
- Dan Ofer
Citations in the corpus
- ProFET: Feature engineering captures high-level protein functions (2015, background): “Currently, there are (cid:2) 27000 such models (InterPro, Mulder and Apweiler, 2007) that cover 83% of all sequences in UniProtKB (2014_10).”
- A beginner's guide to eukaryotic genome annotation (2012, methodology): “…simple approach for obtaining a rough indication of annotation quality is to quantify the percentage of annotations that encode proteins with known domains using tools such as InterProScan 93 and Pfam 94 or tools such as MAKER, which provides an automated means for carrying out such analyses 83 .”
- DOG 1.0: illustrator of protein domain structures (2009, unknown): “For example, the Pfam [1], SMART [2], PROSITE [3], InterPro [4] and other related databases or online tools could predict the functional domain organization of a given protein sequence, and generate the result into a figure.”
- MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis. (2019, methodology): “Mercator relied on sequence similarity and, when appropriate, protein domains from InterPro (Mulder and Apweiler, 2007) and CDD (Marchler-Bauer et al., 2013) that had been manually assigned to the bins.”
- PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees (2012, methodology): “To create the families for a new release, all protein sequences in the new set are scored against the HMMs from the previous release using InterProScan (12), and assigned to the family with best score (viz. the lowest expectation or Evalue) below a significance threshold (E< 0.001).”