Dataset Information

Orfipy: a fast and flexible tool for extracting ORFs.

ABSTRACT:

Summary

Searching 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 https://github.com/urmi-21/orfipy and Bioinformatics online.

SUBMITTER: Singh U

PROVIDER: S-EPMC8479652 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Publications

orfipy: a fast and flexible tool for extracting ORFs.

Singh Urminder U Wurtele Eve Syrkin ES

Bioinformatics (Oxford, England) 20210901 18

<h4>Summary</h4>Searching 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 f ...[more]

PMID: 33576786

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