SPEAR: Systematic ProtEin AnnotatoR

Matthew Crown; Natalia Teruel; Rafael Najmanovich; Matthew Bashton

doi:10.1093/bioinformatics/btac391

SPEAR: Systematic ProtEin AnnotatoR

Matthew Crown, Natalia Teruel, Rafael Najmanovich, Matthew Bashton^*

^*Corresponding author for this work

Applied Sciences

Research output: Contribution to journal › Article › peer-review

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Abstract

Summary
We present SPEAR, a lightweight and rapid SARS-CoV-2 variant annotation and scoring tool, for identifying mutations contributing to potential immune escape and transmissibility (ACE2 binding) at point of sequencing. SPEAR can be used in the field to evaluate genomic surveillance results in real-time and features a powerful interactive data visualisation report.

Availability and implementation
SPEAR and documentation are freely available on GitHub: https://github.com/m-crown/SPEAR and is implemented in Python and installable via Conda environment.

Supplemental
Supplementary data are available at Bioinformatics online.

Original language	English
Article number	btac391
Pages (from-to)	3827–3829
Number of pages	3
Journal	Bioinformatics
Volume	38
Issue number	15
Early online date	13 Jun 2022
DOIs	https://doi.org/10.1093/bioinformatics/btac391
Publication status	Published - 1 Aug 2022

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10.1093/bioinformatics/btac391Licence: CC BY

SPEAR_Application_Note_ResponseAccepted author manuscript, 141 KBLicence: CC BY
Final published versionFinal published version, 389 KBLicence: CC BY
Advance online versionFinal published version, 0.98 MBLicence: CC BY
btac391_supplementary_dataOther version, 1.34 MBLicence: CC BY

Cite this

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title = "SPEAR: Systematic ProtEin AnnotatoR",

abstract = "SummaryWe present SPEAR, a lightweight and rapid SARS-CoV-2 variant annotation and scoring tool, for identifying mutations contributing to potential immune escape and transmissibility (ACE2 binding) at point of sequencing. SPEAR can be used in the field to evaluate genomic surveillance results in real-time and features a powerful interactive data visualisation report.Availability and implementationSPEAR and documentation are freely available on GitHub: https://github.com/m-crown/SPEAR and is implemented in Python and installable via Conda environment.SupplementalSupplementary data are available at Bioinformatics online.",

author = "Matthew Crown and Natalia Teruel and Rafael Najmanovich and Matthew Bashton",

note = "Funding information: MB and MC are funded by Research England{\textquoteright}s Expanding Excellence in England (E3) Fund. MB is funded by the UK Health Security Agency. This work is supported by COG-UK. RJN a member of the R{\'e}seau Qu{\'e}b{\'e}cois de Recherche sur les M{\'e}dicaments (RQRM) and the Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO).",

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doi = "10.1093/bioinformatics/btac391",

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AU - Teruel, Natalia

AU - Najmanovich, Rafael

AU - Bashton, Matthew

N1 - Funding information: MB and MC are funded by Research England’s Expanding Excellence in England (E3) Fund. MB is funded by the UK Health Security Agency. This work is supported by COG-UK. RJN a member of the Réseau Québécois de Recherche sur les Médicaments (RQRM) and the Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO).

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N2 - SummaryWe present SPEAR, a lightweight and rapid SARS-CoV-2 variant annotation and scoring tool, for identifying mutations contributing to potential immune escape and transmissibility (ACE2 binding) at point of sequencing. SPEAR can be used in the field to evaluate genomic surveillance results in real-time and features a powerful interactive data visualisation report.Availability and implementationSPEAR and documentation are freely available on GitHub: https://github.com/m-crown/SPEAR and is implemented in Python and installable via Conda environment.SupplementalSupplementary data are available at Bioinformatics online.

AB - SummaryWe present SPEAR, a lightweight and rapid SARS-CoV-2 variant annotation and scoring tool, for identifying mutations contributing to potential immune escape and transmissibility (ACE2 binding) at point of sequencing. SPEAR can be used in the field to evaluate genomic surveillance results in real-time and features a powerful interactive data visualisation report.Availability and implementationSPEAR and documentation are freely available on GitHub: https://github.com/m-crown/SPEAR and is implemented in Python and installable via Conda environment.SupplementalSupplementary data are available at Bioinformatics online.

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JF - Bioinformatics

SN - 1367-4803

IS - 15

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SPEAR: Systematic ProtEin AnnotatoR

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