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Download
The AAstrech package, the ancillary scrips and programs and the manual can be dowloaded from GitHub:
github.com/matteoramazzotti/AAstretch
Installation instructions
AAstrech is entirely written in perl, so you will need perl to be installed into the system. Only base modules are used, so a minimal perl installation is sufficient for
most purposes.
AAexplore (used to explore the results of AAstretch) takes advantage of two graphic libraries: Tk and GD. Both can be easily instellaed from CPAN.
All the .pl scripts must be placed in the working directory, along with the organisms specific genomic file, that can be obtained from the Organisms page (unzip) or with
AAprepare (see instruction below or the AAstretch manual).
Quick start
- Open your terminal (shell or prompt or whatever) and cd to the working folder. Inside there you should find AAstretch.pl, AAsync.pl, AAstretch.conf and your favorite
organism files (both protein and coding sequence), say organism.prot and organism.cod
- Edit the AAstretch.conf file according to your needs (see the manual).
- Launch AAstretch with "perl AAstretch.pl", then press 1 [enter] to run the scanning
- Look at the results file, particularly to that labelleld with -AAstretch.txt
- If needed, edit the AAstretch.conf, then go to point 3 to rerun the analysis with modified parameters
- Press 4 to "isolate" the results (i.e. separate the newly created files into a dedicated folder)
- Rename that folder with a meaninigful name
- Analyze the output files with text editors, the -AAstretch.txt file with a spreadsheet manager or with AAexplore
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