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ASAFind identifies nuclear-encoded plastid proteins in algae with secondary plastids of the red lineage based on the output of SignalP and the identification of conserved "ASAFAP"-motifs and transit peptides. A web-based version of ASAFind can be found at http://rocaplab.ocean.washington.edu/tools/asafind.

Download

We recommend Version 1.1.7.
You may wish to use the latest Development Version which is less tested.
The published version is Version 1.0.0.
If you need another specific version, click here and click "tags."

Installation Instructions

Install Prerequisites:

  • Python 2.7 or later.
  • Biopython. Developed and tested using v1.63. Subsequent versions are likely to work.

Install ASAFind:

Download and uncompress ASAFind. From the uncompressed directory, move ASAFind.py file to a directory in your PATH (such as /usr/local/bin). If your version of python is not at /usr/bin/python then adjust the first line of ASAFind.py to reflect your system's python path.

Usage Tips

Help

ASAFind.py -h

Inputs

Takes a Fasta and companion SignalP file (versions 3.0, 4.0 or 4.1) short format file as input, either with the complete SignalP header (two lines starting with '#') or just with the results (first line starts with first sequence name). This tool was developed using 3.0, which remains the recommended version for algae with secondary plastids of the red lineage. Can be tested using the example input files: ASAFind.py -f example.fasta -p example.signalp. You can compare your example output to the expected output found in expected_output.tab.

Sequence Names

SignalP truncates the sequence names to 20 characters. Therefore, ASAFind only considers the first 20 characters of the fasta name, which must be unique within the file. Parts of the fasta name after the 20th character are ignored. Additionally, the fasta name may not contain - or | because SignalP changes them to _. If you discover any other characters that SignalP silently changes, please let us know

Minimium Sequence Lengths

ASAFind requires at least 7 aa upstream and 22 aa downstream of the cleavage site identified by SignalP, no prediction is possible for sequences not meeting these requirements.

Citation

If you use ASAFind in your research please cite our publication Gruber et al., doi: 10.1111/tpj.12734 as well as the publications for the appropriate SignalP versions (Petersen et al., doi: 10.1038/nmeth.1701 for SignalP 4.1 or Bendtsen et al., doi: 10.1016/j.jmb.2004.05.028 for SignalP 3.0).

Contact:

cmckay@uw.edu