Downloads for "Filling Gaps in Bacterial Amino Acid Biosynthesis Pathways with High-throughput Genetics"
The easiest way to view the mutant fitness data is with the Fitness Browser. You can also download the mutant fitness data for each organism here:
Further information about most of these organisms and mutant libraries is available here, but the mutant library for Herbaspirillum seropedicae is new.
You can also download an R image containing all of the data here. This was built using lib/comb.R from the RB-TnSeq code base, and some documentation is available there. You can also see the R code for the figures here.
- Protein sequences for H. seropedicae
- Essential proteins in H. seropedicae (Supplementary Table 2)
- scaffoldId, begin, end, strand -- The location of the gene. begin < end regardless of strand
- locusId, sysName, desc -- information about the protein-coding gene.
- GC -- genes' fraction of G or C nucleotides
- nReads -- total number of TnSeq reads that lie within the gene.
- normreads -- nReads normalized to so that the median across all genes is 1, and also normalized for GC content
- nPosCentral -- number of locations within the central 10-90% of the gene that are supported by at least 2 TnSeq reads
- dens -- the density of central insertions, normalized so that the median across all genes is 1
- Strain usage files for H. seropedicae (gzipped tarball)
List of Gaps
Supplementary Table 1 (excel format) lists the steps in amino acid synthesis that were not identified by the IMG web site for all 10 bacteria.
Sanger reads for the hisD region of Azospirillum brasilense Sp245 are available here.
Morgan Price, Arkin group, November 2016