In 2014, my grad student at the time Shu Chen, and I began contemplating the idea of an online repository for weed species genomics information. We were neck deep in assembled transcriptomes — most of which we assembled to find only one gene associated with herbicide resistance. To us it seemed like a waste of resources just to let the data sit around not being used. Of course we uploaded data to NCBI TSA, but this data is of little use to those who do not work with transcriptomes, in bioinformatics, or with large text files (these files are also available on our site by the way). What we saw as a need was a search able database that would allow for searching of any keyword to find genes of interest. But who would use such a site?
WeedGenomics was developed for non-genetics researchers in mind. With the keyword search, researchers could easily find target-site herbicide resistance genes such as “acetolactate synthase” or “psbA”, or any other gene for that matter. Users can search transcriptomes by nucleotide sequence as well with sequences presented in order of most similar. Results can be downloaded in FASTA format allowing easy use of data. Sequences can also be subjected to BLASTn at NCBI or BLASTp via local Uniprot Virdiplantae protein database. Once sequences are identified they can be downloaded in FASTA format or our new trinBank format. I also offer a python script that can be used to create an object from the trinBank file, thus making it easy to use sequences in programs such as Biopython.
Just getting started
The Weed Genomics repository is just getting started. The goal is to grow WeedGenomics into an online community of users that allows for uploading of user data including capillary sequence data, transcriptome assemblies, and genome assemblies. Tools are being developed that allow users to search for SNPs associated with herbicide resistance on the site, with complimentary command line tools for processing large numbers of sequences. See my GitHub site for further information on command line tools (MutationFinder command line). Other tools and information are being added to the site in the coming months. Please let me know what you find useful, what you would like to see developed, and any other ideas for the development of the site. I am always open to new ideas.
So check out the site and let me know what you think.