ASAP
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| ASAP | |
| Who: | Nicole Perna, Univ. of Wisconsin (as standalone system)
As part of ERIC, ASAP is hosted at SRA International. |
| What: | 'Comprehensive community based |
| Where: | ASAP |
| Updates | |
| Upcoming events | link to event calendar, if applicable |
| Web Services | |
About ASAP
ASAP is a comprehensive source of genome information for several enteric bacteria, including E. coli K-12 MG1655 and W3110. ASAP annotations are based on community annotation curated by ASAP staff.
Content
Content at ASAP covers genomes of many enteric bacteria, and is very extensive for individual genomes. ASAP includes:
- Annotations generated by ASAP curators and user community. These are therefore nonredundant with other sites.
- Experimental data, primarily from the Blattner lab
- Strain descriptions from the Blattner lab
ASAP has a page that lists feature types and annotation types
Using ASAP
Browsing
ASAP has its own genome browser, which runs as a Java Applet. On some browsers, this does not open to the selected gene, and does not allow clicking to a nearby gene page. ASAP also includes a Synteny Browser.
Searching
Entering ASAP brings up a query page that allows a fairly customizable search. Most users will probably use two kinds of searches, Location and Basic Options
by Location
Enter the boundaries of the desired location and submit.
by Feature (gene) name
A simple search on gene names is done by entering the name into feature name. Submitting the query brings up a list of features matching the query. The table includes the genome coordinates for any genes found. ASAP recognizes synonyms. For example, searching for groP returns pages for dnaK, dnaJ, and dnaB. T
Restricting the search by feature type
You can restrict the type of feature by selecting one or more feature types from a menu. For example, if you want to
- see all of the rRNA genes, select rRNA and submit the form.
- see only tRNAs between 200kbp and 500kbp, select tRNAs while using 200000 and 500000 in the Chromosome Location section.
Displaying the Results
Clicking on a feature link brings up a display for that feature. The feature pages are in two frames. The left frame has links to a variety of information. The right page has lists of Annotations, Overlapping Features, Orthologs and Paralogs, Similarity Searches, Molecular Interactions, and Experimental Data. feature ID mapped to gene name (https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=114900
Usage examples
Add links to additional pages describing success stories here.
Technology
ASAP is written in PHP. The original Univ. of WIsconsin version uses an underlying MySQL database; the ERIC version migrates this to Oracle.
ASAP offers downloadable data in different forms.
Web Services/API
Not available?
Discussion
References
J. D. Glasner, P. Liss, G. Plunkett III, A. Darling, T. Prasad, M. Rusch, A. Byrnes, M. Gilson, B. Biehl, F. R. Blattner, & N. T. Perna (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31(1):147-151. PubMed full text abstract