RICE DATABASE apikliujkiyhkuyhkuhji.pptx

Rice

1. Rap-db(rice annotation project data base) By Pr asad Praseetha Priya Praveen Kumar Pritheesh

2. Important features Provides the scientific community with accurate and timely annotation of rice genome sequence. was conceptualized in 2004 upon the completion of the  Oryza sativa  ssp.   japonica  cv.  Nipponbare genome sequencing by the International Rice Genome Sequencing Project. One of the major objectives of this project is to facilitate a comprehensive analysis of the genome structure and function of rice on the basis of the annotation.

3. Tools of RAP-DB On the home page of RAP-DB, we find different tools like: 1.BLAST 2.BLAT 3.ID CONVERTER 4.BATCH RETRIEVAL

4. BLAST Executes blast against the rice genome or gene. BLAST gives a selectable search for the given gene to be compared. Options to search from-DNA or PROTEIN db, different blasts like blastn, tblastn, tblstx. Advanced options like expected value cut of, type of score matrix and number of results.

5. BLAT BLAT helps in aligning the given sequence with the sequences from the RAP-DB. It gives a comprehensive analysis by comparing the gene to the whole database and gives different kinds of similar sequences.

6. ID converter- It helps to convert the ID’S of the genes from MSU to RAP or vice versa. Keyword search- A search bar which enables us to find a gene just by typing a name onto it. Several results pop up, similar to the query Batch retrieval- Specific known data can be retrieved using batch retrieval.(the information may include the sequence or the position , function of the gene).

7. GBrowse GBrowse is a very specific tool used to browse the genes and genome of rice. This tool has options like browser, select tracks, snapshots which help the user to identify and find the information about the genes they have searched. They find detailed information of the genes and genome like the precise location , the number of the chromosome, predicted genes , repeat genes etc.

8. Other Features RAP-DB has other features like: Downloads-enables the user to download data from the database. Publications-this contains the research papers and books which can be accessed by the user. Links-this provides links to other features rice databases, RAP-DB members, IRGSP members, related rice resources and other databases like NCBI,DDBJ etc. making the site user friendly. Documents-this contains information on gene statistics, genome statistics, gene nomenclature etc.