ArticleBioinformatics (Oxford, England)2021
orfipy: a fast and flexible tool for extracting ORFs.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
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- Integrative multi-omics analysis widens annotation and functional insights into long non-coding RNAs of Arabidopsis thaliana.Biology direct · 2026Article
- ToxIR: an accurate RNA-seq pipeline for high-precision toxin transcriptome profiling, validated in odontobuthus doriae venom glands.Scientific reports · 2025Article
- Multiple human enhancer RNAs contain long translated open reading frames.Genes & development · 2025Article
- Evolution of the egg glue protein in great ape lice inferred from its sequence comparisons across five louse types.Scientific reports · 2025Article
- Insights into platypus crural gland transcriptomics - venom and beyond.BMC genomics · 2025Article
- TRB proteins in moss reveal their evolutionarily conserved roles in plant development and telomere maintenance.The Plant journal : for cell and molecular biology · 2025Article
- De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods.Genome biology and evolution · 2025Review
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- The Annotated Blueprint: Integrated Functional Genomic Resources for a model Tetraploid WheatbioRxiv : the preprint server for biology · 2025Article
- The Proteomic and Peptidomic Response of Wheat (Plants (Basel, Switzerland) · 2025Article
- Genomic language models (gLMs) decode bacterial genomes for improved gene prediction and translation initiation site identification.Briefings in bioinformatics · 2025Article
- Discovery of novel non-retroviral endogenous viral elements reveals their long-term integration history in spiders.Nature communications · 2025Article
Corrections and comments
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2 authors.
Funding
Abstract
summarySearching for open reading frames is a routine task and a critical step prior to annotating protein coding regions in newly sequenced genomes or de novo transcriptome assemblies. With the tremendous increase in genomic and transcriptomic data, faster tools are needed to handle large input datasets. These tools should be versatile enough to fine-tune search criteria and allow efficient downstream analysis. Here we present a new python based tool, orfipy, which allows the user to flexibly search for open reading frames in genomic and transcriptomic sequences. The search is rapid and is fully customizable, with a choice of FASTA and BED output formats. AVAILABILITY AND IMPLEMENTATION: orfipy is implemented in python and is compatible with python v3.6 and higher. Source code: https://github.com/urmi-21/orfipy. Installation: from the source, or via PyPi (https://pypi.org/project/orfipy) or bioconda (https://anaconda.org/bioconda/orfipy). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.