The first step is to prepare protein sequence databases by translating the RefSeq DNA into all six frames: genome NC_004088, and plasmids NC_004836, NC_004837, NC_004838.
After compression is complete, CaBLASTP can then translate the decreased redundancy of the database into a speed-up when performing search, which is the second phase.
Amino acid sequences derived from genes identified as being involved in the Calvin cycle and the RTCA cycle were used as query sequences to search the translated nucleotide database from the genomes of the A. ferrooxidans DSM 16786, A. thiooxidans DSM 17318 and L. ferriphilum DSM 17947 strains using tBlastn [ 107] with default parameters.
The Indian database translates the verses from Sanskrit to modern languages, updating the names of plants and diseases and grouping them into standard patent classifications.
Therefore, all analyses against the protein databases were also done using FASTY (E-value cutoff: 1.0e-6) a version of FASTA that compares a DNA sequence to a protein sequence database, translates the DNA sequence in three forward (or reverse) frames and allows (in contrast to BLASTX) for frame shifts, maximizing the length of the resulting alignments.
These numbers do not include co-citations where both databases translated the protein groups (complexes) into sets of binary interactions, which we could not systematically trace, and which we suspect may contribute to some of the remaining cases of low S PPI, mainly due to different conventions used to perform the translation.
A tBLASTN search against the translated GenBank database using the C-terminal segment of YabE as query, revealed similar sequences in more than 40 proteins, suggesting that this is a distinct domain, which we have denoted Sps (Stationary phase survival – see below).
Therefore, TBLASTN was performed to search the translated nucleotide database constituted of the different studied genomes using the proteomes as queries [ 37].
As multiple URLs could refer to the same publication, we mapped every URL hit by an automatic query to the PubMed database and translated the URL into a PubMed identifier whenever possible.
As the interviews were conducted in Sinhalese, the researchers (SH, CS) jointly translated the answers to English before database entry was conducted.
