Table 3.
Online Chlamydomonas resources
| Database | URL | Summary |
|---|---|---|
| Phytozome [27] | http://www.phytozome.net | Primary repository of Chlamydomonas genome/gene models. Bulk retrieval of annotation data. Structured to enable comparative genomics with other plants and algae. Contains user validated annotations, and PFAM, Panther and GO predicted annotations. |
| UCLA algal genomics portal | http://genomes.mcdb.ucla.edu/ | Chlamydomonas genome browser. Repository for multiple transcriptomic datasets. |
| Algal Annotation Tool [45] | http://pathways.mcdb.ucla.edu/algal/index.html | Batch conversion of gene identifiers. Bulk annotation prediction via Kegg, MapMan, GO, Panther, Metacyc. |
| GIAVAP | https://giavap-genomes.ibpc.fr/chlamydomonas | Comparison of v5.5 gene predictions with previous versions, browser with BAC and fosmid ends. |
| Iomiqs [29] | http://iomiqsweb1.bio.uni-kl.de | Bulk annotation prediction via MapMan with visual output. |
| Predalgo [31] | https://giavap-genomes.ibpc.fr/cgi-bin/predalgodb.perl?page=main | Green algal-specific protein localization predictions. |
| BioCyc [46] | http://biocyc.org/CHLAMY/organism-summary | Maps gene products onto metabolic pathways. |
| Chlamydomonas Connection | http://www.chlamy.org/ | A Gateway to Resources for Chlamydomonas Research: news, methods, jobs, gene nomenclature etc. |
| Chloroplast genome [47] | http://www.chlamy.org/chloro | Map and gene lists. |
| Flagellar proteome [17] | http://labs.umassmed.edu/chlamyfp/index.php | Based on version 3, but lists JGIv4 equivalence; UMASS Amherst. |
| Kazusa Institute [10] [11] | http://est.kazusa.or.jp/en/plant/chlamy/EST | Distributes cDNA clones corresponding to their EST collection. |
| Chlamydomonas Resource Center | http://chlamycollection.org/ | Distributes strains, plasmids, cDNA libraries, kits etc. |
| ChlamyStation | http://chlamystation.free.fr/ | Paris (IBPC) Collection of photosynthesis mutants. |
| Transcription factors | http://plntfdb.bio.uni-potsdam.de/v3.0/index.php?sp_id=CRE4 | Part of the Plant Transcription Factor Database, University of Potsdam. |
| Silencing RNAs [48] | http://cresirna.cmp.uea.ac.uk/ | from the Sainsbury Laboratory, D.C.Baulcombe group. |
| Green Genie2 [49] | http://stormo.wustl.edu/GreenGenie2/ | Green genie gene models. |
| Plant TFDB [50] | http://planttfdb.cbi.pku.edu.cn/index.php?sp=Cre | Database of Chlamydomonas transcription factors |