What's New

Build #44c news, 30 July 2019

• We generated a unified standard nomenclature system for the vertebrate ORs. For this we developed the Maximum Mutual Similarity (MMS) algorithm which assigns a human-based OR symbols for non-human species, via detecting inter-species hierarchical pairwise similarity relations (Olender T. et.al. BMC Genomics, submitted).
• The algorithm was applied to seven mammals, and to zebrafish. The results were added to HORDE (under "Browse other species").
• The data are also avaliable under download.
• Horse, Zebrafish and Orangutan organism pages have been added with updated nomenclature, including links to NCBI-Gene.

Build #44 news

• Build #44 is based on Hg. 38 coordinates.
• Build #44 uses lucene based index and search engine, allowing even faster searches.
• Links to HGNC is available for each gene.
• Mouse and Rat organism pages have been added with updated nomenclature, including links to NCBI-Gene.

Build #43 news

• Build #43 is based on Hg. 19 coordinates.
• Build #43 has a completely novel design and interface using the PHP5 language and Apache server technologies.
• Data are now stored in a MySQL format allowing faster searches.
• The interface is written in Cakephp as the MVC (model-view-controller) framework and as the ORM (object-relational-mapping) layer.
• Gene Model- To supply information about the complete OR gene structure, HORDE now includes information that is extracted from AicView (http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/).
• The variation information was expanded to include data from: DGV, 1000GP, dbSNP, and the studies of Hasin et. al. 2008, and Waszak et. al. 2010..
• The organisms OR repertoire have a new graphical user interface, and allows the user to easily browse the OR genes for each organism.

Build #42 news

• OR genes were mapped to the assembly hg. 18.
• CORP - Classifier for Olfactory Receptor Pseudogenes. A new tool which assesses the probability of an OR gene with intact open reading frame to encode a non-functional protein.
• CLICs- We developed a novel algorithm which identified 48 conserved clusters (CL usters I n Conservation) in five mammalian genome.
• The opossum OR repertoire was deciphered and analyzed.
• Dog OR repertoire- a new version (V2) is released and contains more than 100 novel ORs.

Build #41 news

• OR genes were mapped to the assembly hg. 17.
• Number of SNP in ORs increased from 1856 to 3395.
• Putative structural properties are provided.
• Information about gene structure is provided when possible.

Build #40 news

Build #40 is a true effort to define a complete non-redundent set of all human ORs, out of the complete human genome assembly (hg 16). It contains 846 genes.

• The sequences of all genes were downloaded and re-translated. We have designed a novel algorithm to allocate the most approporiate ATG and stop codons. The algorithm uses a multiple alignment of mouse and human OR proteins.
• 55 novel genes were defined.
• Redundent ORs were merged.
• Several new features were developed, or are now in development and will be added soon. These are: information about canine ORs, experiment evidances for expression of ORs, and SNPs.

Build #39 news

• 112 novel OR genes.
• Improved OR genomic locations. For each OR gene HORDE is now indicating> a coordinate in bases, based on UCSC human genome assembly, and UDB.
• Information about cluster organization of the OR sub-genome. Most ORs are located in clusters. We define a cluster as a group of genes with inter-genic distance less then 0.8 Mb.
• Link to ORDB.
• Information about mouse OR closest sequences.