Nitrogen is an essential macromolecule for plant growth and development. Atmospheric nitrogen is inert, and thus must be converted—or fixed—in a process that frees up the nitrogen atoms to be used in biosynthesis. Legume-nodulating bacteria (rhizobia) are key players in plant nitrogen fixation, playing a symbiotic relationship with legumes for nitrogen uptake. Specific srRNA (small regulatory RNA) in Sinorhizobium meliloti have been proposed to influence the nitrogen fixation of its plant host.
Mutant strains must therefore be created in a manner that excludes genes of interest, to test this hypothesis, and be re-inserted back into the host’s genome for recombination. After the creation of plausible mutants, the cloned fragment must be sequenced and verified to omit the gene. Sequence analysis should yield two BLAST hits for each sequence: one matching the flanking region of the gene on the left, and the other matching the flanking region of the gene on the right to the reference genome. This ensures that the gene sequence is omitted in the cloned fragment, as well as verifying that the cloned fragment contains a correct match to the reference sequence.
The goal is to automate the process using a command-line program that goes through all the sequences and BLASTs them and checks the corresponding hit values.
The major benefit is that more accurate identification on hundreds of plausible mutant sequences can be performed with a reduction in analyses run time and an increase in accuracy.
Developer | Bioinformatician – Decoding the world, one line at a time.
Highly motivated developer predominantly working in Linux and developing software tools. All about open source software and fascinated by working with multitudes of technologies and languages. Striving to make a positive impact in this world.