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CHOMP – CRISPR Search Tool

CHOMP 🐊 CRISPR Tool CHOMP will search for all ’n’ window sized guide RNAs (gRNAs) sequences containing an NGG at the tail end. Default window size is 23. ex.) ATGTAGCTAGCTAGCTAGTAGGG. It will report how many occurrences of this sequence are present in the target sequence (off-target sites), along with number of matching bases for each subject/query hit. You can use that to determine which gRNAs you may want to use as CRISPR target(s).

Monday, February 6, 2017 | 2 minutes Read
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Tango

#Tango Download source code by clicking Tango title above or here. Please check that the list of dependencies below are locally installed before running. ##Usage Collect, store, and retrieve Genbank records from NCBI with just the GI number. Using NCBI’s E-Utilities interface to fetch records and MongoDB as a local database for storage, the program essentially curates a local database that only contains the records you need with the most significant information. This facilitates maintaining a very specific dataset that can be accessed in downstream analysis. No more looking up NCBI files again!

Friday, October 2, 2015 | 3 minutes Read
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Scripter

Need to write a Perl script? How about a Ruby, Python, or C file? You know it’s not a hard task per say, but do you really want to create the file, enter the standard system variables, your personalized template, and change permissions all in separate steps? You’re already on your way to typing a whole lot more, assuming you are generating this file to code your new idea off course …

Monday, September 29, 2014 | 2 minutes Read
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Sequencher

[embed]https://github.com/bretonics/sequencher\[/embed\] The ever-present need of having to get your sequences’ complementary, reverse, and reverse complementary sequences sparked this project. Yes, you can find online tools, input your sequence, and get results. However, being that I constantly use the bash terminal, and the fact that it’s just simply faster to call a program, add an argument, and hit enter to get a result…well, a native tool is far better than looking for a GUI program.

Monday, August 25, 2014 | 1 minute Read