.. _Field Reference: Field Reference ====================== .. only:: man Field Reference --------------- .. program:: field SINA generates a number of named meta-data values for each processed sequence. By default, all values will be written to ARB output files, while CSV output requires that each meta-data field is specified using :option:`-f/--fields `. The fields generated by SINA and the typical fields present in ARB databases are described below. Basic Fields ~~~~~~~~~~~~ The below fields are standard ARB meta data fields describing each sequence. .. option:: name The ``Id`` of the sequence. In FASTA input and output, this value is mapped to the first word of the header line. .. option:: full_name The textual description of the sequence. In FASTA input and output, this value is mapped to all but the first word of the header line. .. option:: acc The sequence accession number. This field is relevant for ARB input/output as together with :option:`start` it defines the unique identity of the sequence when regenerating sequence names. For sequences read from FASTA and written to ARB, SINA will generate a pseud-accession as ``ARB_`` followed by a 8 character hexadecimal CRC32 checksum. This matches the behavior of ARB during FASTA import. .. option:: version The version part of the accession number reference. .. option:: start The start position of the gene sequence with the sequence referenced by the accession number. .. option:: stop The stop position of the gene sequence with the sequence referenced by the accession number. SINA specific fields ~~~~~~~~~~~~~~~~~~~~ .. option:: align_quality_slv The alignment "quality". The alignment score, normalized to remove weighting effects and scaled as integer between 0 and 100. If the alignment for the sequence was copied from an identical match to a reference sequence, the value is set to 100. .. option:: align_cutoff_head_slv The number of unaligned basepairs at the beginning of the sequence. .. option:: align_cutoff_tail_slv The number of unaligned basepairs at the end of the sequence. .. option:: aligned_slv The time and date at which the sequence was aligned. .. option:: align_startpos_slv The position of the first base of the sequence within the reference alignment. .. option:: align_stoppos_slv The position of the last base of the sequence within the reference alignment. .. option:: align_ident_slv The highest fractional identity of the aligned sequence with any of the used reference sequences. The value is computed using optimistic IUPAC comparison (N matches anything) over the overlapping region of each pair of sequences. .. option:: nuc_gene_slv The number of basepairs aligned within the gene. (Currently not computed). .. option:: align_bp_score_slv A score indicating the average binding strength of basepairs aligned into helix regions. Each pair of bases aligned to opposing sides of a helix specified in the reference database is assigned a score (``AG`` = 0.5, ``AU`` = 1.1, ``CG`` = 1.5, ``GG`` = 0.4, ``GU`` = 0.9), the sum of scores divided by the number of helix positions with bases on either side and multiplied by 100. .. option:: align_family_slv The reference sequences used to align the query sequence. Each reference is listed as ``ACC.START:SCORE`` where ``ACC`` and ``START`` are the contents of the reference sequence's respective :option:`acc` and :option:`start` fields and ``SCORE`` is the score assigned by the sequence search engine (ARB PT server or internal kmer search). .. option:: align_log_slv A log of events that occurred during the alignment of a query sequence. .. option:: align_filter_slv The weighting filter selected for the query sequence, if any. .. option:: nearest_slv The results from the sequence search. Available only when the search stage is enabled (:option:`-S/--search `). Each matched sequence is given as ``ACC.VERSION.START.STOP~SCORE`` where ``ACC``, ``VERSION``, ``START``, and ``STOP`` are the contents of the matched sequence's respective :option:`acc`, :option:`version`, :option:`start` and :option:`stop` fields and ``SCORE`` is the score calculated according to the search settings. SILVA taxonomy fields: ~~~~~~~~~~~~~~~~~~~~~~ The SILVA SSU and LSU databases in ARB format contain taxonomic meta data suitable for generating taxonomic assingments using the :option:``--lca-fields`` option. Each of the following fields contains the taxonomic assignment as a "materialized path" (``Domain; Phylum; ...``). The ``_name`` field contains the sequence name assigned by the respective taxonomy. .. option:: tax_slv The `SILVA `_ taxonomy. .. option:: tax_embl The `EMBL-EBI/ENA `_ taxonomy. Note that the name was changed to `tax_embl_ebi_ena` in newer releases of SILVA. .. option:: tax_embl_ebi_ena The `EMBL-EBI/ENA `_ taxonomy. .. option:: tax_ltp The `Living Tree Project (LTP) `_ taxonomy. .. option:: tax_gg The Greengenes taxonomy. (Discontinued) .. option:: tax_rdp The `RDP II `_ taxonomy. .. option:: tax_gtdb The `Genome Taxonomy Database `_ Taxonomy. Additional standard ARB fields: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. option:: ali_16s/data The actual sequence alignment. This field type always has the form ``ali_/data``, with ```` indicating the alignment (ARB databases may contain multiple alignments). .. option:: ARB_color A number indicating in which color the sequence should be highlighted inside of ARB. .. option:: used_rels The :option:`names ` of the reference sequences used during alignment separated by spaces. This field is generated only if :option:`--write-used-rels ` is given. It allows selecting the reference sequences via a special menu item from within ARB. .. option:: nuc The length of the sequence.