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DiProDB

http://diprodb.fli-leibniz.de/

Description :
Database for dinucleotide properties

GyDB

http://gydb.uv.es/gydb/intro.htm

Description :
Gypsy database of mobile genetic elements

UgMicroSatdb

http://ipu.ac.in/usbt/UgMicroSatdb.htm

Description :
UniGene MicroSatellite database: short tandem repeats from various eukaryotic genomes

PAZAR

http://www.pazar.info/

Description :
Transcription factors and regulatory sequence annotations

DNAreplication.net

http://www.dnareplication.net/

Description :
Database for the eukaryotic DNA replication community

CRISPRcompar

http://crispr.u-psud.fr/CRISPRcompar/

Description :
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements are used in CRISPRcompar as a genetic marker for comparative and evolutionary analysis of closely related bacterial strains.

dbRES

http://bioinfo.au.tsinghua.edu.cn/dbRES/

Description :
Although a large amount of experimentally-derived information about RNA editing sites currently exists, this information has remained scattered in a variety of sources and in diverse data formats. Availability of standard collections for high-quality experimental data will be great helpful for systematic studying of RNA editing, especially for developing computational algorithm to predict RNA editing site. dbRES (http://bioinfo.au.tsinghua.edu.cn/dbRES) is a public database of known RNA editing sites. All sites are manually curated from literature and GenBank annotations. dbRES version 1.1 contains 5437 RNA editing sites of 251 transcripts, covering 96 organisms across plant, metazoan, protozoa, fungi and virus. dbRES provides comprehensive annotations and data summaries, including (but not limited to) transcript sequences, RNA editing types, editing site locations, amino acid changes, organisms, subcellular organelles (if available), cited references, etc. A user-friendly web interface is developed to facilitate both retrieving data and online display of RNA edit site information.

Aknowledgement :
This work is supported partially by The National Basic Research Program (2004CB518605) and National Science Foundation of China (60405001 and 60572086).

References :
1. Gott, J.M. (2003) Expanding genome capacity via RNA editing. C R Biol, 326, 901-908.

AtGDB

http://www.plantgdb.org/AtGDB

Description :
AtGDB is being developed as a part of our NSF-funded project "PlantGDB - Plant Genome Database and Analysis Tools". The purpose of this resource is to provide a convenient sequence-centered genome view for Arabidopsis thaliana, with a narrow focus on gene structure annotation. At AtGDB, you can browse the genome or zoom in on our favorite genes, look at the current gene structure annotation and compare it with cDNA and EST evidence, and (if necessary) contribute your corrections and comments directly to the database. You can access all functions of AtGDB over the web, but you can also download the entire database and interface and install it off-line on your laptop, for example. The premise of this design is that a lot of fun and useful research on the genome-scale is greatly facilitated by a database backend (with all the standard query capabilities) and nice viewing tools.

Aknowledgement :
AtGDB is supported by the U.S.A. National Science Foundation Plant Genome Research grant DBI-0321600.

References :
1. Zhu,W., Schlueter,S.D., Brendel,V. (2003) Refined annotation of the Arabidopsis thaliana genome by complete EST mapping. Plant Physiology 132, 469-484.

RAP-DB

http://rapdb.lab.nig.ac.jp/

Description :
With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating and manually curating all the genes in the rice genome. Here we present the Rice Annotation Project Database (RAP-DB), which has been developed to provide access to the annotation data. The RAP-DB has two different types of annotation viewers, BLAST and BLAT search, and other useful features. By connecting the annotations to other rice genomics data, such as full-length cDNAs and Tos17 mutant lines, the RAP-DB serves as a hub for rice genomics. All of the resources can be accessed through http://rapdb.lab.nig.ac.jp/.

Aknowledgement :
We thank the IRGSP and RAP members for their supports. This work was supported in part by a grant from the special Coordination Funds for Promoting Science and Technology of the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan. Funding to pay the Open Access publication charges for this article was provided by a grant from the NIAS Genebank Project.

References :
1. Moore,G., Devos,K.M., Wang,Z. and Gale,M.D. (1995) Cereal genome evolution. Grasses, line up and form a circle. Curr. Biol., 5, 737-739.
2. Sasaki,T. and Burr,B. (2000) International Rice Genome Sequencing Project: the effort to completely sequence the rice genome. Curr. Opin. Plant Biol., 3, 138-141.
3. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature, 436, 793-800.
4. Yuan,Q., Ouyang,S., Wang,A., Zhu,W., Maiti,R., Lin,H., Hamilton,J., Haas,B., Sultana,R., Cheung,F. et al. (2005) The institute for genomic research Osa1 rice genome annotation database. Plant Physiol., 138, 18-26.
5. Kikuchi,S., Satoh,K., Nagata,T., Kawagashira,N., Doi,K., Kishimoto,N., Yazaki,J., Ishikawa,M., Yamada,H., Ooka,H. et al. (2003) Collection, mapping, and annotation of over 28 000 cDNA clones from japonica rice. Science, 301, 376-379.
6. Miyao,A., Tanaka,K., Murata,K., Sawaki,H., Takeda,S., Abe,K., Shinozuka,Y., Onosato,K. and Hirochika,H. (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell, 15, 1771-1780.
7. Stein,L.D., Mungall,C., Shu,S., Caudy,M., Mangone,M., Day,A., Nickerson,E., Stajich,J.E., Harris,T.W., Arva,A. et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res., 12, 1599-1610.
8. Imanishi,T., Itoh,T., Suzuki,Y., O Donovan,C., Fukuchi,S., Koyanagi,K.O., Barrero,R.A., Tamura,T., Yamaguchi-Kabata,Y., Tanino,M. et al. (2004) Integrative annotation of 21 037 human genes validated by full-length cDNA clones. PLoS Biol., 2, e162.
9. Kent,W.J. (2002) BLAT--the BLAST-like alignment tool. Genome Res., 12, 656-664.
10. Altschul,S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
11. Dowell,R.D., Jokerst,R.M., Day,A., Eddy,S.R. and Stein,L. (2001) The distributed annotation system. BMC Bioinformatics, 2, 7.

Rice Annotation Database

http://golgi.gs.dna.affrc.go.jp/SY-1102/rad/index.html

Description :
Contig data for manual annotation of rice genome

RiceGAAS

http://ricegaas.dna.affrc.go.jp/

Description :
Rice genome automated annotation system

Aknowledgement :
The development of this system was supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Rice Genome Project SY1101, SY1103, GS-1302).

Apollo Genome Annotation and Curation Tool

http://www.fruitfly.org/annot/apollo/

Description :
Apollo is a genome annotation viewer and editor. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment.

Artemis

http://www.sanger.ac.uk/Software/Artemis/

Description :
DNA sequence viewer and annotation tool; allows visualization of sequence features and results of analyses within the context of the sequence and its 6-frame translation; available for UNIX, Windows and Macintosh.

BASys

http://wishart.biology.ualberta.ca/basys/

Description :
BASys (Bacterial Annotation System) is a tool for automated annotation of bacterial genomic (chromosomal and plasmid) sequences including gene/protein names, GO functions, COG functions, possible paralogues and orthologues, molecular weights, isoelectric points, operon structures, subcellular localization, signal peptides, transmembrane regions, secondary structures, 3-D structures, reactions, and pathways.

Bioverse

http://bioverse.compbio.washington.edu/

Description :
Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

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