dbRES: A web-oriented database for annotated RNA Editing Sites

dbRES: Quick guide for web users

Browsing dbRES

    dbRES can be browsed using 2 method: by species tree or by RNA editing types. Click the BROWSE link on the left bar to activate the browser for species. The browser for species organize the information in a form lile a NCBI taxonomy tree.

    The tree can be expand level by level along with the users clicking on the links. In the deepest level of the tree, the species name is shown in "<>", following with a number in "()" showing the amount of RNA editing event of this species. Expanding this level will get a list of NCBI gene names. Clicking on these names will lead users to a database navigation page.

    At the same time, by clicking on the link "type of RNA editing site", users can get a page listing all 9 kinds of RNA editing mentioned by dbRES. And expanding any of this type will get a list of NCBI gene names corresponding to the expanded RNA editing type. And a further clicking action will lead user to database navigation page.

Quick navigation inside dbRES

    Once users get into the page called Database Viewer, a quick cross navigation function can be used. In the shown breif table of dbRES records. Several fields are marked as hyper links. The link of RESDB ID can lead users to see the details of dbRES records. By clicking on the Accession No., A page called Transcript Viewer will be shown. And clicking on other links will guide users to view the full list of corresponing RNA editing sites.

    The transcript viewer will show the transcript the user asked for. All the corresponding RNA editing site will be marked as hyper links on transcript sequence. Clicking on these hyper link will lead users to the dbRES record viewer.

    The record viewer shows the detail of any RESDB records. A link to NCBI or MiRBase corresponding record is provided as well. And the PubMed abstract of corresponding reference literature can be linked from record viewer directly.

BLAST dbRES

    dbRES can be searched by using a query sequence, A server side blast system will search the database to generae a accession number list for the user. If you find anything wrong of this function, please contact with the webmaster.

Get sequence database

    If users want to use BLAST locally, a hidden web API can be help. By copy the following URL to a the URL text box of browser, you can get a FASTA file contain all transcript inside dbRES.

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

    Then just save the shown page as a ASCII Text file, you can get a complet sequence database of dbRES in FASTA format. This FASTA file only contain accession no. and sequence. The RNA editing site information need to be retrieved from dbRES downloading function.

Download data package

    Go to DOWNLOAD page for details.