2009-07-15

• Webcode
  • Remove guestbook due to too many access for that from nowhere.
• Database
  • Add the 48 nucelear receptor genes (from Yogita) into candidate target gene list.

• Webcode
  • Use cookie to save user's setting. The default storage time is 3 hours from now.

• Webcode
  • Fix the bug for 1-to-2 HCNE display. Now only color those multi-copies HCNEs on different chromosome: change to use "select count(distinct(chr1))...", instead of "select count(*)...". But this will bring another potential problem: those paralog HCNEs ending in same chromosome will not be colored, but actually they should be, even though cases like that are minor.
  • Change the color of 1-to-2 HCNEs into orange, the rest into gray.
• Database
  • Use index to speed up the database query (Done by David. Tusen takk)

• Webcode
  • Dropdown list for reference species, including assembly version, is added beside the query input.
  • Other reference species except human in the preference page is disabled. A warning message will prompt when the user select them.
  • Input region bigger than 10M bp will be double-confirmed by pop-up dialog. Also, input coordinate with end less than start will be alerted.
  • The previous option for multiple ortholog sets is too confusing. Now, we change to use Ensembl ortholog set as the main one, but put "include exonAlign prediction" and "exclude out-paralog" as two options to choose.
  • Add "Site history", which is the page you are reading.

• Webcode
  • Gene synonyms are added as possible search keyword. For example, input 'wagr' will also return "PAX6" since it's one of synonyms of PAX6 (See here)
  • A bug was fixed that in the tree view, the name of the main gene is an Ensembl ID while on the browser the name is the gene symbol. (reported by one of the reviewers)
  • An option is added in preferences to highlight HCNEs that overlap in reference genome coordinates (1-to-many HCNEs) in a different color. By default this option is not activated.
  • For each HCNE, a link to its corresponding alignment page in Ancora is added.
• Database
  • Gene synonyms dataset is extracted from BioMart(hg18, Ensembl v53) and used in Synorth. It's saved as flatfile @ $DATADIR/ensemblGene_synonym_v49_hg18.txt
  • HCNE dataset (from Ancora) for hg18 vs. five teleost genomes are formated and stored in Synorth MySQL db, with table name: cne_twoWay_${spe}_${speRef}_len50_id700_v1

• Webcode
  • Website name is changed from "GRB(GRB Evolution Browser)" to "Synorth(A browser for GRB evolution)". The logo is also changed.
  • Help pages are spell-checked again. Thanks for the group member, eps. David/Christopher/Ying
  • New guest comment page is installed. Spam message can be stopped. (Guestbook v2.0)
• Database
  • Flatfile database for comments

• Webcode
  • Ortholog set with filtering the out-paralog is added.
  • It's possible to leave comments for the guests. (Guestbook v1.0)