HSE_sequence_finder/CITATION.cff at main · cabbi-bio/HSE_sequence_finder · GitHub

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cff-version: 1.2.0
message: "If you use this software, please cite it as below."
type: software
title: "DNA/RNA Sequence Pattern Finder"
abstract: "A Python tool for searching specific patterns in DNA/RNA sequences with support for mismatches, variable gap sizes, and comprehensive statistical analysis. Designed for promoter analysis, cis-regulatory element discovery, and transcription factor binding site identification."
authors:
  - family-names: "Qiande"
    given-names: "Moni"
    email: "mqiande@ufl.edu"
    affiliation: "University of Florida"
    orcid: "https://orcid.org/0000-0002-9797-4367"
version: "1.0.0"
date-released: "2025-10-11"
license: Apache-2.0
repository-code: "https://github.com/qiandemoni/HSE_sequence_finder"
keywords:
  - bioinformatics
  - DNA sequence analysis
  - RNA sequence analysis
  - transcription factor binding sites
  - promoter analysis
  - cis-regulatory elements
  - motif discovery
  - pattern matching
  - computational biology
references:
  - type: article
    title: "PlantCARE, a database of plant cis-acting regulatory elements"
    authors:
      - family-names: Lescot
        given-names: Magali
    journal: "Nucleic Acids Research"
    year: 2002
    doi: "10.1093/nar/30.1.325"
  - type: article
    title: "PlantPAN 4.0: updated database for identifying conserved non-coding sequences"
    authors:
      - family-names: Chow
        given-names: Chi-Nga
    journal: "Nucleic Acids Research"
    year: 2024
    doi: "10.1093/nar/gkad1066"