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ASAP

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Link/URL:

A Systematic Annotation Package (ASAP)

What:

Comprehensive genome information for several enteric bacteria with community annotation.


Who:

Nicole Perna, Univ. of Wisconsin

Updates:
Upcoming events:
Web Services:


Contents

About ASAP

Home Page

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, including published microarray and proteomic data.
  • 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

File:ASAP query.jpg
ASAP query page
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.

Other sites with related content

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

None available

Discussion

ASAP has lots of important content. For example, it is easy in ASAP to find the locations of different kinds of features, even if you can't always search for them by name. For example, by selecting prophage, you can find the locations of 10 cryptic prophage in MG1655. However, you can't find specific prophage by searching for e14 or rac. By contrast, searching for rac in EcoCyc does return hits. But it's easier to see how many prophage are there using ASAP; EcoCyc returns hits for every prophage gene when you search for "prophage".

ASAP can be frustrating in some cases from problems with its user interface. For example, in the simple query page, the search box for ASAP FeatureID(s) is prominently placed but is going to be used rarely by naive users (it is not clear to me who uses that search field at all JimHu 06:27, 4 July 2006 (CDT)). If they do type a gene name there, they will get no hits. Feature name is also nonintuitive as a surrogate for gene name. ASAP also can surprise the user with links that lead to long load times. For example, clicking on Published Annotation in the Annotation lists often loads the entire genome record from NCBI. Loading the genome and synteny browsers can also be so slow that the user may think that the program is not responding.

References

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See Help:References for how to manage references in EcoliWiki.

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

External Links

Discussion of ASAP on other websites