Submitting Author: Semidán Robaina (@Robaina)
All current maintainers: @Robaina
Package Name: Pynteny
One-Line Description of Package: Query sequence database by HMMs arranged in predefined synteny structure
Repository Link: https://github.com/Robaina/Pynteny
Version submitted: v0.0.5
Editor: @arianesasso
Reviewer 1: @Batalex
Reviewer 2: @c-thoben
Archive:
JOSS DOI:
Version accepted: 1.0.0
Date accepted (month-day-year): 03-10-2023

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Description

• Include a brief paragraph describing what your package does:j

Pynteny is Python tool to search for synteny blocks in (prokaryotic) sequence data through HMMs of the ORFs of interest and HMMER. By leveraging genomic context information, Pynteny can be employed to decrease the uncertainty of functional annotation of unlabelled sequence data due to the effect of paralogs. Pynteny can be accessed (i) through the command line, (ii) as a Python module, or (iii) as a (locally served) web application.

Scope

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  • Data retrieval
  • Data extraction
  • Data munging
  • Data deposition
  • Data visualization
  • Reproducibility
  • Geospatial
  • Education
  • Unsure/Other (explain below)

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Pynteny's main objective is to provide a means to query NGS (unannotated) sequence databases, such as metagenomic/metatranscriptomic datasets using syntenic blocks (i.e. spatial arrangements of genes) rather than single target genes/protein domains. In this sense, I would classify Pynteny within Data Extraction.

• Who is the target audience, and what are the scientific applications of this package?

Pynteny was designed to be used by researchers working with large, unannotated sequence databases, such as those typically encountered in metagenomic analyses. It can be accessed through a command line interface or easily integrated into pipelines as a Python package. Pynteny can also be used through a graphical interface running locally in the browser, which is more suitable for educational purposes.

• Are there other Python packages that accomplish similar things? If so, how does yours differ?

To the extent of my knowledge, there isn't any Python package that provides the functionality provided by Pynteny.

• If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussions or @tag the editor you contacted: Pynteny: a Python package to perform synteny-aware, profile HMM-based searches in sequence databases #65

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