Tag: UniGene

The UniGene web pages are now retired

As we previously announced,  we planned to retire the UniGene web pages at the end of July, 2019.   All UniGene pages now redirect to this post. We have also removed links to UniGene from the NCBI home page and other resources.

Although the web pages are no longer available, you will still be able to download the final UniGene builds as static content from the FTP site.  You will also be able to match UniGene cluster numbers to Gene records by searching Gene with UniGene cluster numbers. For best results, restrict to the “UniGene Cluster Number” field rather than all fields in Gene.  For example, a search with Mm.2108[UniGene Cluster Number] finds the mouse  transthyretin Gene record (Ttr).  You can use the advanced search page to help construct these searches. Keep in mind that the Gene record contains selected Reference Sequences and GenBank mRNA sequences rather than the larger set of expressed sequences in the UniGene cluster.

Please write to us with any comments, concerns, or if you need help using UniGene data.

NCBI to Retire the UniGene Database

In July 2019, we will retire the UniGene database and take down the web interface.

UniGene was originally implemented as a gene-oriented grouping of transcript sequences in the absence of a reference genome for a broad range of organisms. We added genome-based grouping later.

UniGene has since been used as a source of approximate expression profiles, an index of available cDNA clones, and as a guide to transcript-oriented resource design. However, with the advent of short read sequencing, fewer and fewer ESTs are submitted to NCBI every year, and reference genomes are available for most organisms with a sizable research community. Consequently, the usage of and need for UniGene has dropped significantly.

Although we will retire the web interfaces, we will continue to have the most recent UniGene builds available on NCBI’s FTP site.  Web traffic to UniGene entries will redirect to relevant gene entries when those are available. When that’s not possible, web requests will be routed to either a representative nucleotide sequence entry or a helpful Entrez query against nucleotide records.

Please contact us at info@ncbi.nlm.nih.gov with any comments, concerns, or if you need help with the use of UniGene data.