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orfipy: a fast and flexible tool for extracting ORFs
Link to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2020.10.20.348052v1?rss=1
Authors: Singh, U., Wurtele, E. S.
Abstract:
Searching for ORFs in transcripts is a critical step prior to annotating coding regions in newly-sequenced genomes and to search for alternative reading frames within known genes. With the tremendous increase in RNA-Seq 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 fasta 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). Contact: [email protected], [email protected] Supplementary information: Supplementary data are available at https://github.com/urmi-21/orfipy .
Copy rights belong to original authors. Visit the link for more info
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By Multimodal LLCLink to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2020.10.20.348052v1?rss=1
Authors: Singh, U., Wurtele, E. S.
Abstract:
Searching for ORFs in transcripts is a critical step prior to annotating coding regions in newly-sequenced genomes and to search for alternative reading frames within known genes. With the tremendous increase in RNA-Seq 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 fasta 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). Contact: [email protected], [email protected] Supplementary information: Supplementary data are available at https://github.com/urmi-21/orfipy .
Copy rights belong to original authors. Visit the link for more info