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:
and the studies of
Hasin et. al. 2008,
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
- 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
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.