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Frequently Asked Questions about the TIGR Rice Resource
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1. What is the subspecies of the rice annotated at TIGR? 2. What is the most direct way to locate a rice sequence relative to the centromere? 3. Why are some BAC/PACs not found in pseudomolecules? 4. Do you have data files for rice intergenic sequences, 5'UTR and 3'UTR respectively? 5. How to obtain the corresponding locus ID and GenBank accession number of a gene? 6. How to find the genetic markers anchored for a specific BAC/PAC clone? 7. How to get the physical position for a specific BAC/PAC clone? 9. Why are some models missing from the ftp files? 10. Can I order an EST clone from you? 11. Can I order a BAC/PAC clone from you? 12. How do you determine the cM position for a BAC/PAC clone? 13. How to find the coordinates for the exons and cds for each gene model? 14. How were the pseudomolecules created? 15. Which gene identifier should I use? 16. How do I download TIGR rice genome annotation data? 17. Do you have a parser for your XML annotation format? 18. How do I refer to the TIGR Rice Genome Annotation Resource? 19. What is the difference between the TIGR pseudomolecules and those of the IRGSP? 20. Is the TIGR annotation the same as that of the Rice Annotation Project (RAP)? 21. My locus identifier has disappeared in the new release. Where can I find my locus? 1. What is the subspecies of the rice annotated at TIGR? Back to top We use the sequence of the International Rice Genome Sequencing Project, that of Oryza sativa spp japonica cv Nipponbare. 2. What is the most direct way to locate a rice sequence relative to the centromere? Back to top You can use monocot centromere specific rice satellite repeat sequence CentO (GenBank accession: AF058902) to identify the centromeres on the pseudomolecules. In addition, fluorescent in situ hybridization information has also been used to map the centromeres. 3. Why are some BAC/PACs not found in pseudomolecules? Back to top We were not able to incorporate all BAC/PAC clones into our pseudomolecules for several reasons. For example, some of the BAC/PACs are from indica, not japonica rice. Others are unfinished sequence. However, other BAC/PAC clones that are publicly available in Genbank/DDBJ/EMBL could not be incorporated into our pseudomolecules as:
Those unused BAC/PAC can be retrieved at http://rice.tigr.org/tdb/e2k1/osa1/unusedBAC/unusedBAC.shtml . As new builds of our pseudomolecules occur, we will incorporate the non-redundant unmapped BAC/PAC clones into the tiling path. Note that our pseudomolecules do not represent the official pseudomolecules generated by the IRGSP. 4. Do you have data files for rice intergenic sequences, 5'UTR and 3'UTR respectively? Back to top We have files containing UTR (both 5' and 3') in our ftp site (ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/) when the gene model aligned well with rice EST and/or full-length cDNA sequences (see README ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/README). 5. How to obtain the corresponding locus ID and GenBank accession number of a gene? Back to top We have assigned pub_locus to the rice genes. They can be retrieved at: http://rice.tigr.org/tdb/e2k1/osa1/LocusNameSearch.shtml. We have not submitted the annotation to GenBank unless the sequences have been finished at TIGR. 6. How to find the genetic markers anchored for a specific BAC/PAC clone? Back to top Please see: http://www.tigr.org/tdb/e2k1/osa1/BACmapping/Genetic_Markers_map.shtml. 7. How to get the physical position for a specific BAC/PAC clone? Back to top Please use the information for the specific chromosome, such as: http://rice.tigr.org/tigr-scripts/e2k1/irgsp_orderedBAC.spl?db=osa1&chr=9. 8. I noticed dates for the directories under the pseudomolecule ftp site have changed a few times since their release: is the database still the same? Back to top The dates for the ftp site directories may not reflect the dates of data release. For each version, the README file under each ftp directory states the date for the data release. 9. Why are some models missing from the ftp files? Back to top We excluded the partial genes, pseudogenes, and small gene models (<50 amino acids) in the ftp files from our pseudomolecules. 10. Can I order an EST clone from you? Back to top TIGR does not own the EST clones. We simply obtained the sequence from public domains to build the gene index (OsGI). You can order a clone from the Japanese Ministry of Agriculture, Forestry and Fisheries (MAFF) Genome Projects or RiceGenes or The Arizona Genomics Institute. 11. Can I order a BAC/PAC clone from you? Back to top TIGR does not distribute the physical BAC/PAC clones. The easiest place to obtain a BAC clone would be from the The Arizona Genomics Institute (http://www.genome.arizona.edu/orders/) or RGP (http://rgp.dna.affrc.go.jp/Cloneaccess.html). You can order individual clones online from them by using clone name as catalog number. 12. How do you determine the cM position for a BAC/PAC clone? Back to top We downloaded all rice BAC/PAC sequences from GenBank and searched these sequences against the marker sequences obtained from the Cornell RiceGenes Database and the Japanese Rice Genome Program. The polyA/polyT and Ns at the ends of marker sequences were then trimmed. Using a high stringency cutoff of greater than 97% identity with the marker sequence, we parsed out the BAC/ PAC clones that contained markers and the cM positions were determined by the anchored marker sequences. We used `~' to indicate that there is no marker sequence anchored for that specific BAC/PAC clones. For example, ~98.5 cM was an estimation based on the neighboring clones. We did not convert the map positions in the different maps from Cornell and RGP. We realize that sometimes Cornell and RGP map the same marker to different locations. 13. How to find the coordinates for the exons and cds for each gene model? Back to top You can find this information in the downloadable .coordset files for genes in BAC clones or .xml/gff3 files for genes in the pseudomolecules from TIGR rice ftp site at: ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/. 14. How were the pseudomolecules created? Back to top Pseudomolecules are the virtual contigs constructed by resolving discrepancies between overlapping BAC/PAC clones, trimming the overlap regions, and linking the unique sequences to form a contigous sequence for each rice chromosome. Rice pseudomolecules were generated by using a TIGR in-house, database-based, semi-automatical process. There were several key steps: 1) Overlapping regions between BACs were determined by similarity searches and tiling path information; 2) The pseudomolecules were made by removing the overlapping regions; 3) The gene models and associated features from the BAC/PAC clones were copied from the BAC/PACs to the pseudomolecules; 4) Quality control. 15. Which gene identifier should I use ? Back to top There are several gene identifiers in TIGR rice genome annotation database, such as locus, pub_locus, com_name, TU feat_name, model feat_name. The TU feat_name (such as 11667.t00001) and model feat_name (such as 11667.m00001) are the uid (unique identifier) for a gene in TIGR rice genome annotation database. We have implemented locus ids for Release 3. The convention for Release 3 is LOC_Osxxg##### where X is one of the 12 chromosomes and the # represents sequential loci on the pseudomolecule. Pub_locus (such as LOC_Os01g01010) is a stable identifier for genes across different versions. We encourage you to use locus id. Please note that the feat_name for a gene in the BAC clone differs from the feat_name for the same gene in the pseudomolecule. Due to the continuous updates to most of the unfinished sequences, our automated annotations are also updated continuously and the gene identifiers will change. However, we will keep each version of our pseudomolecule releases in the database and we recommend that the users to use the dataset from pseudomolecules if you wish to trace back the gene models you are interested in. You can track your gene models among our pseudomolecule versions by using our Version Converter. 16. How do I download TIGR rice genome annotation data? Back to top The TIGR Rice Genome Data Download page provides a description of the formats that are available to download rice genome annotation data and a data extractor tool. The data extractor tool allows the selection of coordinates and types of annotation data and creates a zip file of the selected data for download. If you wish to download the entire data set or a number of entire chromosome data sets, please use the FTP site.
17. Do you have a parser for your XML annotation format? Back to top
The pseudomolecules presented on our web pages and FTP site have been generated as part of our National Science Foundation funded Rice Genome Annotation Project. Our pseudomolecules were constructued using all of the BAC/PAC sequences from the IRGSP which are available in Genbank/DDBJ/EMBL. Please note that our pseudomolecules do not represent the official pseudomolecules generated by the IRGSP. 20. Is the TIGR annotation the same as that of the Rice Annotation Project (RAP)? Back to top The TIGR annotation project and the Rice Annotation Project are separate projects focused on annotating the rice genome. Different pseudomolecules and different methods/criteria are used to identify gene models between the two groups. While some of the annotation may be similar between the two groups, the annotation will differ due to the alternative annotation methods used in the two projects. We have mapped the RAP models to our pseudomolecules to allow users to compare annotation between the two projects 21. My locus identifier has disappeared in the new release. Where can I find my locus? Back to top Information about obsolete locus indentifiers can be found at the Obsolete Loci Search. |
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For Rice Comments/Questions
send mail to the TIGR
rice team. |
| Photographs courtesy
of Robin Buell (TIGR), Jiming Jiang (University of Wisconsin), and the USDA Agricultural Research Service |
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