seqname

Seqname is a label used to identify a sequence in biological data sets and related file formats. It typically refers to the name of the sequence’s source, such as a chromosome, a scaffold, a mitochondrial genome, a plasmid, or a transcript, and serves as the primary reference key for the sequence within a dataset.

In common data formats, the seqname appears in different positions. In FASTA and FASTQ, the header line begins with a greater-than symbol followed by a seqname and an optional description; the seqname is the token used to refer to the sequence in subsequent analyses. In GFF and GFF3 files, the first column is the seqname (also called seqid), indicating the sequence on which a feature is located. In many analysis pipelines, the seqname corresponds to the reference sequence’s name in the alignment or assembly. Other formats may use similar terms such as chromosome, contig, or reference ID to denote the same concept.

Naming conventions for seqnames emphasize stability and uniqueness within a dataset. They should avoid spaces and unusual characters, and often use prefixes such as chr or accession-like identifiers to reflect the source. When combining data from multiple sources, it is common practice to canonicalize seqnames to a consistent naming scheme to prevent mismatches.

Practical use of seqnames includes filtering, aggregating, and indexing data by sequence name. Analyses often group features by seqname to produce per-sequence summaries, extract per-sequence subsets, or join annotation with sequence data.

See also: sequence identifier, accession number, locus, chromosome naming, reference sequence.