Homologous sequences were manually extracted, translated and designated as either class I or class II pilE based upon relatedness to known pilin genes and the presence of the SM1 motif (EYYLN) in the translated sequence.
Out of a finally-curated organelle genome all CDS features are extracted, translated into proteins taking all corresponding RNA editing into account and stored as a BLAST database, which can be used for analysis.
The region including the direct repeats and the GAG motif is extracted, translated, and searched for reverse transcriptase motifs and only the candidates that present no Copia or Gypsy reverse transcriptase motifs are retained.
All open reading frames (ORFs) in the 5' to 3' direction at least 150 nucleotides long were extracted, translated, and compared against the annotated set of X. tropicalis genes (JGI, version 4.1 Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA) using BLASTP [ 37] with default settings and including hits of E-value 1e-10 or better.
For each species, all annotations with a completeness and contiguity ≥ 95%% in at least one assembly of each assembler (see Additional file 1: Table S1 for differences in assemblies) were extracted, translated to the corresponding amino acid sequences and validated via BLASTp homology searches against the Refseq proteins.
Most verbatim extracts were translated from French to English, then slightly edited for the purposes of this paper.
CCT consists of several custom Bash and Perl scripts that are used to create a local COG sequence database [ 4], download sequences of interest from NCBI [ 5], extract and translate ORFs, extract CDS feature translations, perform BLAST searches [ 6], assign COG functional categories to proteins, generate CGView XML files [ 7] and create graphical maps.
When acquiring a book, he typically prepares a synopsis, extracts of the original, translated extracts and something about the author and the book's reception in the original language - a package which compares favourably with the information provided by literary agents for many authors writing in English.
Each of these data collections is extracted and translated from the original source to a common data format by expert curators following well-defined procedures.
The corresponding locations in the genomes were extracted and translated into amino acids.
