2Institute for Neuroscience, George Washington University
Browser extensions are small software programs that enhance the user’s online experience by creating greater browser functionality. Here, I present a Caenorhabditis elegans specific extension for Google Chrome browsers. The software is built from four files: 1) an HTML file called celegansChrome.html that generates the user interface; 2) a JavaScript file called celegansChrome.js that contains objects of C. elegans gene data; 3) a JSON file that contains a manifest of the program contents called manifest.json; and 4) a small image file of a C. elegans hermaphrodite called icon.png that gets loaded into the browser toolbar. The software is freely available at the Google Chrome Web Store by simply clicking the add to Chrome link to load the extension into the browser:
chrome.google.com/webstore/detail/celeganschrome/ipnlfcanpnhkhljmminidjndijjmheib
The user can enter a gene common name (e.g., egl-4) and the Chrome extension can provide the user with C. elegans gene data from any website or even while off-line. Often, it’s convenient to retrieve linkage data or interactome data for a specific C. elegans gene while browsing different webpages or reading journal articles online – this extension provides a frictionless interface for the user to retrieve these data without having to open a new tab and search another website or paper for these data. Currently, the extension provides the user with linkage data for C. elegans genes, gene interaction data, human othology data to a C. elegans gene, and also a gene overview using the WormBase (Harris et al., 2014) RESTful API (only this feature requires internet connectivity). The linkage data loaded into the C. elegans Chrome extension was mined from WormMart WS220 (www.wormbase.org/), while the human ortholog data is from the InParanoid program database (Sonnhammer and Ostlund. 2015). The interaction data were downloaded from the WormBase version WS237 ftp site, and the overview of gene data relies on the WormBase RESTful API. The WormBase RESTful API provides access to gene data by creating a URI using standard HTTP requests that is unique to each gene – the unique identifier being a WBID. The C. elegans Chrome extension takes as input the C. elegans gene common name and maps it to the corresponding WBID to generate the unique URI.
This simple browser extension operates as a client-side program (with the exception of the overview option), and thus provides very fast and seamless data retrieval for C. elegans gene data while browsing any site online.
References
Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, et al., (2014). WormBase 2014: New views of curated biology. Nucleic Acids Res. 42: D789-793. 
Sonnhammer EL, and Ostlund G, (2015). InParanoid 8: Orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Res. 43: D234-239.
Batch_Fusion_Primer: a tool to generate the necessary primers for GFP fusion experiments from files containing any number of sequences
Here, I present a simple script written in Perl for generating the necessary primers for use in GFP fusion experiments (Hobert, 2002; Reporter gene fusions) in C. elegans using multi sequence files. The program returns forward and reverse GFP fusion primers based on parameters determined by the user. These parameters include: length of search areas at the 5′ and 3′ ends of the input sequence; forward primer length, and reverse primer length (to be appended to the GFP specific oligo); and 3′ end GC clamp. The main feature of this script is that it works with files containing any number of FASTA formatted DNA sequences. The script uses the BioPerl SeqIO module (Stajich et al., 2002) to parse FASTA formatted sequences, and can easily be adapted to return primers from a large number of formats, including GenBank, EMBL, ABI, FASTQ, and KEGG (Stajich et al., 2002). The program returns primers with GC% between 40 and 60, and primer Tm values between 52°C and 68°C. The program selects against highly repetitive sequences composed of multiple tandem identical base pairs or multiple di-nucleotide repeats. The program also examines self-complementarity within each primer and enumerates a ‘selfie_score’ by generating reverse complement substrings of each primer and checking for pattern matches. Two ‘selfie_score’ values are returned for the fusion primer: the first one examines self-complementarity to the designed reverse primer only, and the second score checks complementarity between the designed portion and also the GFP specific portion.
The script is organized such that parameters for each primer (forward or reverse) can be easily modified (and improved) by the user independently, and contains comments describing each step. The program executes from the command line and the output provides tab separated features that prints to the screen and also writes to an output file: tab1: start position of primer; tab2: primer Tm; tab3: primer sequence; tab4: selfie_score {two scores for the fusion primer}; tab5: percent GC content.
This simple script might be of use to researchers working on multi-gene families, alternatively spliced transcripts, or really any type of large gene data set where GFP expression is desired. If only forward primers are desired the user can enter ‘zero’ for 3′ space to be sampled, and using such modifications to the code may provide further utility in traditional PCR experiments for large gene data sets. Hosted at SourceForge and freely available for download here – http://batchfusionprimerfetch.sourceforge.net/
References
Boulin, T. et al. Reporter gene fusions (April 5, 2006), WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.106.1, http://54.165.141.74/. PubMed
Hobert O. (2002). PCR fusion-based approach to create reporter gene constructs for expression analysis in transgenic C. elegans. Biotechniques 32, 728-30. PubMed
Stajich JE, et al. (2002). The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12, 1611-1618. PubMed