Field Reference

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 -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.

name

The Id of the sequence. In FASTA input and output, this value is mapped to the first word of the header line.

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.

acc

The sequence accession number. This field is relevant for ARB input/output as together with 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.

version

The version part of the accession number reference.

start

The start position of the gene sequence with the sequence referenced by the accession number.

stop

The stop position of the gene sequence with the sequence referenced by the accession number.

SINA specific fields

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.

align_cutoff_head_slv

The number of unaligned basepairs at the beginning of the sequence.

align_cutoff_tail_slv

The number of unaligned basepairs at the end of the sequence.

aligned_slv

The time and date at which the sequence was aligned.

align_startpos_slv

The position of the first base of the sequence within the reference alignment.

align_stoppos_slv

The position of the last base of the sequence within the reference alignment.

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.

nuc_gene_slv

The number of basepairs aligned within the gene. (Currently not computed).

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.

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 acc and start fields and SCORE is the score assigned by the sequence search engine (ARB PT server or internal kmer search).

align_log_slv

A log of events that occurred during the alignment of a query sequence.

align_filter_slv

The weighting filter selected for the query sequence, if any.

nearest_slv

The results from the sequence search. Available only when the search stage is enabled (-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 acc, version, start and 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.

tax_slv

The SILVA taxonomy.

tax_embl

The EMBL-EBI/ENA taxonomy. Note that the name was changed to tax_embl_ebi_ena in newer releases of SILVA.

tax_embl_ebi_ena

The EMBL-EBI/ENA taxonomy.

tax_ltp

The Living Tree Project (LTP) taxonomy.

tax_gg

The Greengenes taxonomy. (Discontinued)

tax_rdp

The RDP II taxonomy.

tax_gtdb

The Genome Taxonomy Database Taxonomy.

Additional standard ARB fields:

ali_16s/data

The actual sequence alignment. This field type always has the form ali_<name>/data, with <name> indicating the alignment (ARB databases may contain multiple alignments).

ARB_color

A number indicating in which color the sequence should be highlighted inside of ARB.

used_rels

The names of the reference sequences used during alignment separated by spaces. This field is generated only if --write-used-rels is given. It allows selecting the reference sequences via a special menu item from within ARB.

nuc

The length of the sequence.