ASRP - Help Page for the ASRP

The Genome Browser can be accessed by clicking on the Genome View link on the top link bar or by clicking on the Home link and then clicking on a region of one of the blue chromosome bars.

How do I use the Genome Browser?

To begin using the browser, type a query into the box labeled "Landmark or Region" or click on one of the example links near the top of the page. The query box has the ability to handle gene accessions (AtXgXXXXX), small RNA database entry numbers (DBE#), genome coordinates (e.g. 1:24416..36433), MIRNA names (e.g. MIR390a), or feature names (e.g. tRNA. Depending on the query, the displayed data will zoom in or out so that the display fits to the size of the query.

The "Scroll/Zoom" tool can be used to increase or decrease the size of the region being displayed. It can also shift the window to the right or left of the current region. The gray bar just below the "Scroll/Zoom" tool displays a representation of the current chromosome. The red box on this bar indicates the chromosomal position of the current window. Clicking anywhere on this box will move the window to the corresponding region of the chromosome. A scale bar for the current region can be found on top of the displayed tracks. Clicking anywhere on the scale bar will recenter the window to that point.

The "Dumps, Searches and other Operations" tool, found underneath the displayed region, can be used to download data from the current display in various formats. The drop-down menu is used to select the desired download tool. Each tool can be configured by clicking on the "Configure" button.

What information is displayed in the Genome Browser?

Data sets displayed in the Genome Browser are separated into data tracks. Tracks can be turned on or off at the bottom of the browser page. A description of each track can be viewed by clicking on the track name.

Searching

What search tools are available?

There are two ways to search for data. The first search tool is the Primary Search Tool which can be found by clicking the search link or the home link in the Main Menu. The second is the Quick Search which is located on the Main Menu of each page. The Quick Search tool can be used to rapidly retrieve data from a single database (i.e. a miRNA # search will retrieve that miRNA's information page). The Primary Search Tool can be used to do cross-database searches. The Quick Search tool can handle gene accessions (AtXgXXXXX), miRNA names (miRXXX), small RNA database entry numbers (DBE#), or short sequences (25 nucleotides or less). The Primary Search Tool can handle gene accessions, miRNA names, genome coordinates (e.g. 1:24416..36433), and sequences up to 5,000 nucleotides long. The Primary Search Tool can also handle multiple queries simultaneously. Note: queries other than sequences should be separated by returns or spaces. Sequences separated by spaces or on separate lines will be concatenated unless they are in fasta format.

What do the search result catagories represent?

All of the categories represent features that overlap the query on the genome. "Sequence(s)" are small RNA sequences, "miRNA" are MIRNA genes, "Gene(s)" are annotated genes in the current release of the Arabidopsis genome, and "tasiRNA" are TAS genes.

How can I download my search results?

After clicking on a search result category a download link will appear that will download the search results for that category in comma separated value (csv) format.

Downloads

What data is available to download?

All of the ASRP small RNA data in total and for specific libraries can be downloaded in precompiled files on the downloads page. miRNA and tasiRNA families, targets, and transcripts are also available for download. In general, data can be downloaded in general feature format (gff), fasta, or comma separated value (csv) formats (Note: some data sets are too large to be imported to Microsoft Excel and are therefore not available in csv format). The entire ASRP database can also be downloaded as a MySQL dump file.

BioMoby

Can the ASRP database be accessed as a web service?

BioMoby web services are established for searches using AGI locus codes for the input query. These services can be accessed using the Taverna project to build workflows for data retrieval.

The ASRP website organizes information about Arabidopsis thaliana small RNAs. It is funded by NSF as a 2010 project. All small RNAs have either been isolated by the ASRP or published by other labs.