[1][2] WormBase is used by the C. elegans research community both as an information resource and as a place to publish and distribute their results.

Many of these changes were single nucleotide insertions or deletions, however several large mis-assemblies have been uncovered.

Other improvements have come from comparing genomic DNA to cDNA sequences and analysis of RNASeq high-throughput data.

The changes in the genomic sequence pose difficulties when comparing chromosomal coordinates of data derived from different releases of WormBase.

[6] All the gene-sets of the WormBase species were initially generated by gene prediction programs.

However, other data types (e.g. protein alignments, ab initio prediction programs, trans-splice leader sites, poly-A signals and addition sites, SAGE and TEC-RED transcript tags, mass-spectroscopic peptides, and conserved protein domains) are useful in refining the structures, especially where expression is low and so transcripts are not sufficiently available.

WormBase encourages researchers to inform them via the help-desk if they have evidence for an incorrect gene structure.

When any change is made to a CDS (or Pseudogene), the old gene model is preserved as a ‘history’ object.

The boundary between what is considered a reasonable coding transcript is sometimes subjective as, in the absence of other evidence, the use of weak splice sites or short exons can often produce a putative, though unsatisfactory, model of a CDS.

Pseudogenes and genes with a problematic structure are constantly under review in WormBase and new evidence is used to try to resolve their status.

Coding Sequences (CDSs) are the only part of a Gene's structure that is manually curated in WormBase.

The transcripts of a gene in WormBase are automatically derived by mapping any available cDNA or mRNA alignments onto the CDS model.

If there are no isoforms of the coding gene, for example AC3.5, but there is alternative splicing in the UTRs, there will be multiple transcripts named AC3.5.1 and AC3.5.2, etc.

Gene trees allow the alignment of orthologues between parasitic worms, other nematodes and non-worm comparator species.

A BioMart data-mining tool is offered to permit large scale access to the data.