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Team:NYC Software/Tools/BLAST
From 2011.igem.org
BLASTing against the Biobricks
When setting off on an iGEM project, it is important to know what parts you are interested in using have already been biobricks and are available in the initial distribution. Searching through the huge numbers of parts by text query is pretty laborious and you sometimes miss the parts you're looking for. Instead, we thought that searching the Registry based on the sequence of a part would be a more direct route.
We coded a python script that will take a sequence and use the BLAST executables to find the most similar parts (or parts of parts) in the current registry.
The code for this program is available on the iGEM Software github repo: NYC SOFTWARE REPO
Our goal was to offer a web-based method for easily browsing through these parts, but at the time of the wiki freeze we do not have this online. Check This Location to see our progress.
Or check out the BLAST utility currently residing on partsregistry.org -> Registry BLAST. This tool will compare you query sequence against those in the Registry, but the interface of the output is relatively simple and is not interactive.
We studied genes responsible for radiation resistance in Deinococcus and E. coli using whole genome analysis to compare frequencies of certain D.rad-related genes in experimental genomes.
The only way for the new field like synthetic biology to grow is to make it easier for new entrants. We contribute to the field by developing tools that ease biobrick project design and allow iGEMers to take to the wetlab more quickly.
Primer Design
