GeoBoost: Accelerating research involving the geospatial metadata of virus GenBank records

Tasnia Tahsin, Davy Weissenbacher, Karen O'Connor, Arjun Magge, Matthew Scotch, Graciela Gonzalez-Hernandez

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

GeoBoost is a command-line software package developed to address sparse or incomplete metadata in GenBank sequence records that relate to the location of the infected host (LOIH) of viruses. Given a set of GenBank accession numbers corresponding to virus GenBank records, GeoBoost extracts, integrates and normalizes geographic information reflecting the LOIH of the viruses using integrated information from GenBank metadata and related full-text publications. In addition, to facilitate probabilistic geospatial modeling, GeoBoost assigns probability scores for each possible LOIH. Availability and implementation Binaries and resources required for running GeoBoost are packed into a single zipped file and freely available for download at https://tinyurl.com/geoboost. A video tutorial is included to help users quickly and easily install and run the software. The software is implemented in Java 1.8, and supported on MS Windows and Linux platforms. Contact gragon@upenn.edu Supplementary informationSupplementary dataare available at Bioinformatics online.

Original languageEnglish (US)
Pages (from-to)1606-1608
Number of pages3
JournalBioinformatics
Volume34
Issue number9
DOIs
StatePublished - May 1 2018

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Nucleic Acid Databases
Metadata
Viruses
Virus
Software
Research
Probabilistic Modeling
Normalize
Linux
Bioinformatics
Software Package
Software packages
Java
Assign
Availability
Computational Biology
Integrate
Contact
Binary
Publications

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Tahsin, T., Weissenbacher, D., O'Connor, K., Magge, A., Scotch, M., & Gonzalez-Hernandez, G. (2018). GeoBoost: Accelerating research involving the geospatial metadata of virus GenBank records. Bioinformatics, 34(9), 1606-1608. https://doi.org/10.1093/bioinformatics/btx799

GeoBoost : Accelerating research involving the geospatial metadata of virus GenBank records. / Tahsin, Tasnia; Weissenbacher, Davy; O'Connor, Karen; Magge, Arjun; Scotch, Matthew; Gonzalez-Hernandez, Graciela.

In: Bioinformatics, Vol. 34, No. 9, 01.05.2018, p. 1606-1608.

Research output: Contribution to journalArticle

Tahsin, T, Weissenbacher, D, O'Connor, K, Magge, A, Scotch, M & Gonzalez-Hernandez, G 2018, 'GeoBoost: Accelerating research involving the geospatial metadata of virus GenBank records', Bioinformatics, vol. 34, no. 9, pp. 1606-1608. https://doi.org/10.1093/bioinformatics/btx799
Tahsin, Tasnia ; Weissenbacher, Davy ; O'Connor, Karen ; Magge, Arjun ; Scotch, Matthew ; Gonzalez-Hernandez, Graciela. / GeoBoost : Accelerating research involving the geospatial metadata of virus GenBank records. In: Bioinformatics. 2018 ; Vol. 34, No. 9. pp. 1606-1608.
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