ASAFind

 

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 downloadable stand-alone version can be found at https://bitbucket.org/rocaplab/asafind

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 . Here is a example fasta input and a example signalp input

Sequence Names

SignalP truncates the sequence names to 20 characters. Therefore, ASAFind only considers the first 20 charcacters 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.

Output

The output of ASAFind is a tab delimited table, with a prediction for each protein.

Input Fasta:
Enter sequences below in FASTA format
Each sequence name must be unique within first 20 characters.

Or upload a fasta file:

 

 

Input companion SignalP data:
Enter output from SignalP in short format (you may omit column headers or leave them in)

Or upload a SignalP output file:

 

 

Output
Standard Format

Short Format

 

 

Ready?

Portable Version
Would you like to run ASAFind locally? Download a stand alone version of this tool.

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).

 

NSF logo

Support for the development of ASAFind provided by the National Science Foundation, the Gordon and Betty Moore Foundation and the German Research Foundation.

Any opinions, findings and conclusions or recomendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the funders.