CO-ARBitrator Rev2 README

17 June 2019: Revision 2 of the CO-ARBitrator data set is available. It is based on a March 21 2019 snapshot of GenBank, and contains 1,286,434 records of which 249,002 are new since the original revision.<br>The release consists of 4 files: a nucleotide fasta, an incremental nucleotide fasta, an amino acid fasta, and a TSV table. In the TSV table, each row describes a sequence and provides nucleotide and amino acid accession #s and sequences as well as taxonomy.<br><br>The defline format of the fasta files has been changed since the original release, hopefully for the better! In rev 1, deflines contained taxonomy copied verbatim from sequence record pages. These taxonomies are lists of values without rank identifiers; intermediate ranks (e.g. suborder or infraorder) may or may not be present. <br>In rev 2, wherever possible, the taxonomy in the fasta deflines has been retrieved from the NCBI taxonomy browser. Where taxonomy is not available, it is deduced from the "organism" field of the sequence's NSBI record.<br>Example defline:<br> p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo; color: #000000; background-color: #ffffff} span.s1 {font-variant-ligatures: no-common-ligatures} &gt;AAG37251|Litoria_nannotis|K_Metazoa__P_Chordata__C_Amphibia__O_Anura__F_Hylidae__G_Litoria__S_nannotis<br>The format is:&gt;Accession|Binomial|TaxonomyTaxonomic ranks are labeled by the first letter of the rank. In the example above, the kingdom (K) is Metazoa, the phylum (P) is Chordata, etc.<br><br>Please address questions, comments, or requests to Phil Heller at [e-mail].