Thirteen versions of 799F were assessed for the exclusion of chloroplast sequences from our samples.
Each of the 158 retrieved Arabidopsis proteins was used as individual query to identify homolog sequences from our local protein database comprising the RefSeq GenBank data and conceptual translations of transcriptomic datasets from diverse eukaryotes, which do not have genome sequence available yet57.
Instead, they are DNA sequences from our mitochondria, the organelles responsible for packaging nutrient energy into a readily accessible form.
Four different strains – ΔserB, ΔgltA, ΔilvA, and Δfes – were rescued by specific sequences from our library.
After stripping vector sequences the files were aligned along with the contig sequences from our assembly and compared visually.
Peptide sequence analysis showed that sequences from our purified protein correlated with the sequence of mouse IL-34 (Figure S1b).
The homologous sequences from our representative set of E. coli genomes were compiled and aligned using ClustalW [109].
In 3(b) the ROC40 plot refers to over 700 sequences from our test set that share no more than 40% sequence identity with first BLAST hits.
To determine to what extent ErbB3 contributes to the divergence of the ErbB family, we ran the BPPS procedure by removing ErbB3 sequences from our alignments.
In the present study, we used Sanger sequence reads obtained from our previously published study [18] and high-throughput 454 sequences from our unpublished neurotoxicity study (see Materials and Methods for details).
First, the almost full-length sequences from our libraries were combined with the closest relatives, cultivated and uncultivated, from databases, aligned, and subjected to phylogenetic analysis using the neighbor-joining method [78].
