A DNA sequence searching tool to parse for DNA sequences for nuclear hormone receptor response elements such as nGREs or other subsequences
Access the tool's website here
The tool uses regular expression based searching to find matches to the nGRE consensus sequence or custom sequences that can contain variability in length, IUPAC codes, and/or mutations within a given gene sequence. The user is also able to input different penalty values for each type of mutation that are subtracted from the match's score that indicates how closely it resembles the sequence of interest. All scored matches are then returned in a dataframe to the user containing information about each matches sequence, location, and number of mutations.
There is currently no other web browser based tool for the searching and scoring of imperfect matches to variable length sequences within gene sequences. This tool allows for the searching of nGREs and other subsequences that have variable length elements within gene sequences and returns comprehensive information about all matches to the subsequence found. Allowing for searching of sequences that have variable length elements such as many nuclear hormone receptor response elements within gene sequences gives scientists an expedited ability to find information about genes' potential abilities to respond to different hormones. The tool being browser-based, only relying on users clicking on a URL, simplifies the utilization process of the tool because there is no necesity of downloading software, launching command-line instructions, and/or using programming languages. The browser-based nature of the tool therefore simplifies a user's experience with the tool and increases the accessibility of the tool to biologists that may not have computational background and/or hardware optimized for running programming-based tools.
To get started with the tool, read the tool's About Tool page. One can then copy and paste a gene sequence of interest into the tool to parse it for nGREs or custom elements.
Users can get help with this project by adding an issue to this repository detailing their question or the perceived shortcoming of the tool.
The tool's creator, @hewittk, maintains and contributes to the project. If you are interested in contributing, please make an issue on this repository