cazy_webscraper: For creating a local CAZy database

Emma Hobbs; Tracey Gloster; Sean Chapman; Leighton Pritchard

doi:10.6084/m9.figshare.14370860.v3

cazy_webscraper: For creating a local CAZy database

Emma Hobbs, Tracey Gloster, Sean Chapman, Leighton Pritchard

Strathclyde Institute Of Pharmacy And Biomedical Sciences

Research output: Contribution to conference › Poster

71 Downloads (Pure)

Abstract

Carbohydrate Active enZymes (CAZymes) are pivotal in pathogen recognition, signalling, structure and energy metabolism. CAZy (www.cazy.org) is the most comprehensive CAZyme database, but it does not provide methods for automating data retrieval or submitting sequences for annotation.

cazy_webscraper retrieves user-specified datasets from CAZy, producing a local SQL database enabling thorough interrogation of the data. cazy_webscraper can also retrieve protein sequences from GenBank and download structure files from RCSB PDB.

Original language	English
DOIs	https://doi.org/10.6084/m9.figshare.14370860.v3
Publication status	Published - 4 Apr 2021
Event	Microbiology Society Annual Conference 2021 - Online Duration: 26 Apr 2021 → 30 Apr 2021 https://microbiologysociety.org/event/annual-conference/annual-conference-online-2021.html

Conference

Conference	Microbiology Society Annual Conference 2021
Period	26/04/21 → 30/04/21
Internet address	https://microbiologysociety.org/event/annual-conference/annual-conference-online-2021.html

Keywords

bioinformatics
CAZyme
CAZymes
CAZy
CAZy proteins
CAZy protein families
webscraper
CAZy family

Access to Document

10.6084/m9.figshare.14370860.v3Licence: CC BY 4.0

Hobbs-etal-MSAC-2021-cazy-webscraper-For-creating-a-local-CAZy-databaseOther version, 0.98 MBLicence: CC BY 4.0

1 Poster
1 Article
1 Working paper

cazy_webscraper: local compilation and interrogation of comprehensive CAZyme datasets
Hobbs, E. E. M., Gloster, T. M. & Pritchard, L., 14 Aug 2023, In: Microbial Genomics. 9, 8, 23 p., 001086.
Research output: Contribution to journal › Article › peer-review

Open Access
File
3 Citations (Scopus)

21 Downloads (Pure)
cazy_webscraper: local compilation and interrogation of comprehensive CAZyme datasets
Hobbs, E. E. M., Gloster, T. M. & Pritchard, L., 3 Dec 2022, (Submitted) Long Island, New York, NY, USA, 19 p.
Research output: Working paper

File
85 Downloads (Pure)
Comprehensive evaluation of CAZyme prediction tools in fungal and bacterial species
Hobbs, E., Gloster, T., Chapman, S. & Pritchard, L., 4 Apr 2021.
Research output: Contribution to conference › Poster

Open Access
File
84 Downloads (Pure)

1 Education Outreach

PhD Supervision
Gloster, T. (Advisor), Pritchard, L. (Advisor), Chapman, S. (Advisor) & Hobbs, E. (Recipient)
1 Sept 2019 → 1 Sept 2023
Activity: Public Engagement and Outreach › Education Outreach

Cite this

@conference{96b3656cc670428ea79ef20abfbc7aac,

title = "cazy_webscraper: For creating a local CAZy database",

abstract = "Carbohydrate Active enZymes (CAZymes) are pivotal in pathogen recognition, signalling, structure and energy metabolism. CAZy (www.cazy.org) is the most comprehensive CAZyme database, but it does not provide methods for automating data retrieval or submitting sequences for annotation.cazy_webscraper retrieves user-specified datasets from CAZy, producing a local SQL database enabling thorough interrogation of the data. cazy_webscraper can also retrieve protein sequences from GenBank and download structure files from RCSB PDB.",

keywords = "bioinformatics, CAZyme, CAZymes, CAZy, CAZy proteins, CAZy protein families, webscraper, CAZy family",

author = "Emma Hobbs and Tracey Gloster and Sean Chapman and Leighton Pritchard",

year = "2021",

month = apr,

day = "4",

doi = "10.6084/m9.figshare.14370860.v3",

language = "English",

note = "Microbiology Society Annual Conference 2021 ; Conference date: 26-04-2021 Through 30-04-2021",

url = "https://microbiologysociety.org/event/annual-conference/annual-conference-online-2021.html",

}

TY - CONF

T1 - cazy_webscraper

T2 - Microbiology Society Annual Conference 2021

AU - Hobbs, Emma

AU - Gloster, Tracey

AU - Chapman, Sean

AU - Pritchard, Leighton

PY - 2021/4/4

Y1 - 2021/4/4

N2 - Carbohydrate Active enZymes (CAZymes) are pivotal in pathogen recognition, signalling, structure and energy metabolism. CAZy (www.cazy.org) is the most comprehensive CAZyme database, but it does not provide methods for automating data retrieval or submitting sequences for annotation.cazy_webscraper retrieves user-specified datasets from CAZy, producing a local SQL database enabling thorough interrogation of the data. cazy_webscraper can also retrieve protein sequences from GenBank and download structure files from RCSB PDB.

AB - Carbohydrate Active enZymes (CAZymes) are pivotal in pathogen recognition, signalling, structure and energy metabolism. CAZy (www.cazy.org) is the most comprehensive CAZyme database, but it does not provide methods for automating data retrieval or submitting sequences for annotation.cazy_webscraper retrieves user-specified datasets from CAZy, producing a local SQL database enabling thorough interrogation of the data. cazy_webscraper can also retrieve protein sequences from GenBank and download structure files from RCSB PDB.

KW - bioinformatics

KW - CAZyme

KW - CAZymes

KW - CAZy

KW - CAZy proteins

KW - CAZy protein families

KW - webscraper

KW - CAZy family

U2 - 10.6084/m9.figshare.14370860.v3

DO - 10.6084/m9.figshare.14370860.v3

M3 - Poster

Y2 - 26 April 2021 through 30 April 2021

ER -

cazy_webscraper: For creating a local CAZy database

Abstract

Conference

Keywords

Access to Document

Fingerprint

Research output

cazy_webscraper: local compilation and interrogation of comprehensive CAZyme datasets

cazy_webscraper: local compilation and interrogation of comprehensive CAZyme datasets

Comprehensive evaluation of CAZyme prediction tools in fungal and bacterial species

Activities

PhD Supervision

Cite this