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Journal Articles Nucleic Acids Research Year : 2023

SulfAtlas, the sulfatase database: state of the art and new developments

Abstract

SulfAtlas (https://sulfatlas.sb-roscoff.fr/) is a knowledge-based resource dedicated to a sequence-based classification of sulfatases. Currently four sulfatase families exist (S1–S4) and the largest family (S1, formylglycine-dependent sulfatases) is divided into subfamilies by a phylogenetic approach, each subfamily corresponding to either a single characterized specificity (or few specificities in some cases) or to unknown substrates. Sequences are linked to their biochemical and structural information according to an expert scrutiny of the available literature. Database browsing was initially made possible both through a keyword search engine and a specific sequence similarity (BLAST) server. In this article, we will briefly summarize the experimental progresses in the sulfatase field in the last 6 years. To improve and speed up the (sub)family assignment of sulfatases in (meta)genomic data, we have developed a new, freely-accessible search engine using Hidden Markov model (HMM) for each (sub)family. This new tool (SulfAtlas HMM) is also a key part of the internal pipeline used to regularly update the database. SulfAtlas resource has indeed significantly grown since its creation in 2016, from 4550 sequences to 162 430 sequences in August 2022.
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Dates and versions

hal-03948623 , version 1 (20-01-2023)

Licence

Attribution - NonCommercial

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Mark Stam, Pernelle Lelièvre, Mark Hoebeke, Erwan Corre, Tristan Barbeyron, et al.. SulfAtlas, the sulfatase database: state of the art and new developments. Nucleic Acids Research, 2023, 51 (D1), pp.D647-D653. ⟨10.1093/nar/gkac977⟩. ⟨hal-03948623⟩
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