https://github.com/linsalrob/adapt
ADAPT presents a web-based system for the analysis of ARISA data sets
https://github.com/linsalrob/adapt
Last synced: 2 months ago
JSON representation
ADAPT presents a web-based system for the analysis of ARISA data sets
- Host: GitHub
- URL: https://github.com/linsalrob/adapt
- Owner: linsalrob
- License: mit
- Created: 2017-08-30T22:28:00.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2017-08-30T22:44:31.000Z (almost 9 years ago)
- Last Synced: 2026-03-29T13:46:45.654Z (3 months ago)
- Language: Perl
- Homepage: https://edwards.sdsu.edu/adapt
- Size: 1.73 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# ADAPT
[ADAPT](https://edwards.sdsu.edu/cgi-bin/adapt-test/ADAPTHome.cgi) (#A#RISA #D#ata #A#nalysis program for #P#athogenic and #T#rophic comparison) is a web-application and was originally developed and designed for the data analysis needs of the Rohwer Lab at San Diego State University (SDSU) by Rob Schmieder in 2009. ADAPT was further developed to fit the needs of researchers in other labs.
ADAPT is a web-based bioinformatics tool to taxonomically characterize ARISA data sets by comparing the ARISA profiles to our existing ADAPTdb database. Based on the comparison results, the program provides the user with a likely representation of what species are in the analyzed samples. Additionally, the program also performs pathogenicity and autotrophic/heterotrophic comparisons of organisms among different ARISA samples using the additional organism information for each 16S-ITS-23S region in the ADAPTdb database, and provides a table and graphical representation of the autotrophic/heterotrophic and the pathogenic/non-pathogenic average fraction for each sample.
If the input file contains data from more than one sample, ADAPT also compares the profiles between samples to highlight similarities and differences among those samples
[ADAPT](https://edwards.sdsu.edu/cgi-bin/adapt-test/ADAPTHome.cgi) is described in the unpublished [pre-print](https://edwards.sdsu.edu/research/wp-content/uploads/2011/02/RobSchmieder_ADAPT.pdf) that was reviewed but not published. You can find the reviews, and a comment on the reviews on our [lab blog](https://edwards.sdsu.edu/research/adapt/). We are not going to publish the paper.
# ADAPT Code
We have been asked to provide the adapt code for others to build upon. It is provided in a working state, and this is the code directly from our [ADAPT webserver](https://edwards.sdsu.edu/adapt)
# AS-IS Code
This code is provided as-is. We are not supporting it, and are unlikely to provide any updates to this code. It may break your system, it may delete your files. You are responsible for understanding what it does and using it appropriately. We are not liable.