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[[Category:Databases]] | [[Category:Databases]] | ||
[[Category:E. coli Databases]] | [[Category:E. coli Databases]] | ||
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{| {{Prettytable}} width='30%' align="right" id="B497edd17ef856" class=" tableEdit Database_table" | |||
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!align=left {{table heading style}} |Link/URL: | |||
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[https://asap.ahabs.wisc.edu/asap/logon.php A Systematic Annotation Package (ASAP)] | |||
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!align=left {{table heading style}} |What: | |||
| Comprehensive genome information for several enteric bacteria with community annotation. | || | ||
Comprehensive genome information for several enteric bacteria with community annotation. | |||
|- | |- | ||
| | !align=left {{table heading style}} |Who: | ||
| | || | ||
Nicole Perna, Univ. of Wisconsin | |||
|- | |- | ||
| Updates | !align=left {{table heading style}} |Updates: | ||
| | || | ||
|- | |- | ||
| Upcoming events | !align=left {{table heading style}} |Upcoming events: | ||
| | || | ||
|- | |- | ||
| Web Services | !align=left {{table heading style}} |Web Services: | ||
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|- class="tableEdit_footer" | |||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.1635.B497edd17ef856&page=1635&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table]</span> || | |||
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=About {{PAGENAME}}= | <!--box uid=63ce1649aab8b3180235b0af7618f667.1635.B497edd17ef856--></protect> | ||
==About {{PAGENAME}}== | |||
[[Image:ASAP_home.jpg|right|Home Page|thumb|350px]] | |||
[http://asap.ahabs.wisc.edu/asap/home.php {{PAGENAME}}] 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. | [http://asap.ahabs.wisc.edu/asap/home.php {{PAGENAME}}] 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== | ||
Content at ASAP covers genomes of many enteric bacteria, and is very extensive for individual genomes. ASAP includes: | 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. | :*Annotations generated by ASAP curators and user community. These are therefore nonredundant with other sites. | ||
:*Experimental data, | :*Experimental data, including published microarray and proteomic data. | ||
:*Strain descriptions from the Blattner lab | :*Strain descriptions from the Blattner lab | ||
ASAP has a page that [https://asap.ahabs.wisc.edu/asap/db_summary.php?LocationID=&SequenceVersionID=&GenomeID=&ExpSetID=#WIS_MG1655 lists feature types and annotation types] | ASAP has a page that [https://asap.ahabs.wisc.edu/asap/db_summary.php?LocationID=&SequenceVersionID=&GenomeID=&ExpSetID=#WIS_MG1655 lists feature types and annotation types] | ||
=Using {{PAGENAME}}= | ==Using {{PAGENAME}}== | ||
==Browsing== | ==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. | 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== | ===Searching=== | ||
[[Image:ASAP_query.jpg|thumb|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 | [[Image:ASAP_query.jpg|thumb|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=== | ====by Location==== | ||
Enter the boundaries of the desired location and submit. | Enter the boundaries of the desired location and submit. | ||
===by Feature (gene) name=== | ====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 | 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 | ||
| Line 51: | Line 72: | ||
*see only tRNAs between 200kbp and 500kbp, select tRNAs while using 200000 and 500000 in the Chromosome Location section. | *see only tRNAs between 200kbp and 500kbp, select tRNAs while using 200000 and 500000 in the Chromosome Location section. | ||
===Displaying the Results=== | ====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. | 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 | feature ID mapped to gene name (https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=114900 | ||
==Usage examples== | ===Usage examples=== | ||
''Add links to additional pages describing success stories here.'' | ''Add links to additional pages describing success stories here.'' | ||
=Other sites with related content= | =Other sites with related content= | ||
=Technology= | ==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 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. | ASAP offers downloadable data in different forms. | ||
==Web Services/API== | ===Web Services/API=== | ||
None available | None available | ||
=Discussion= | ==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 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 [[User:JimHu|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. | 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 [[User:JimHu|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= | ==References== | ||
{{BacktoTop}} | |||
{{RefHelp}} | |||
<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. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=12519969 PubMed] [http://nar.oupjournals.org/cgi/content/full/31/1/147 full text] [http://nar.oupjournals.org/cgi/content/abstract/31/1/147 abstract] | 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. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=12519969 PubMed] [http://nar.oupjournals.org/cgi/content/full/31/1/147 full text] [http://nar.oupjournals.org/cgi/content/abstract/31/1/147 abstract] | ||
==External Links== | |||
=External Links= | |||
*[http://asap.ahabs.wisc.edu/software/asap/ {{PAGENAME}} project page] | *[http://asap.ahabs.wisc.edu/software/asap/ {{PAGENAME}} project page] | ||
*[http://asap.ahabs.wisc.edu/asap/home.php {{PAGENAME}} at the University of Wisconsin] | *[http://asap.ahabs.wisc.edu/asap/home.php {{PAGENAME}} at the University of Wisconsin] | ||
*[http://www.ericbrc.org/ | *[http://www.ericbrc.org/ {{PAGENAME}} as part of ERIC] | ||
==Discussion of {{PAGENAME}} on other websites== | ==Discussion of {{PAGENAME}} on other websites== | ||
Latest revision as of 00:11, 23 May 2010
You can help EcoliWiki by editing the content of this page. For information about becoming a registered user and obtaining editing privileges, see Help:Accounts.
| Link/URL: | |
|---|---|
| What: |
Comprehensive genome information for several enteric bacteria with community annotation.
|
| Who: |
Nicole Perna, Univ. of Wisconsin |
| Updates: | |
| Upcoming events: | |
| Web Services: |
|
| edit table |
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, 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
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
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
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