Ancient-Rep will find internal TMS repeats using a list of homologs.

Enter ‘ancient’ in the Terminal app to begin.

This is the Ancient program. This tool will find very old (and new) TMS repeat
units. Results can be viewed as they become      available by using the
readlive.py command. Alignments can be viewed using the show_alignment.py
command. This tool was created by:     Vamsee Reddy, 2010 Saierlab
<Symphony.Dev@gmail.com> :: http://projectv.tcdb.org

Options:
  --version            show program's version number and exit
  -h, --help           show this help message and exit
  -i INPUT             Path to your subject fasta file
  -r REPEAT            Repeat Size
  -o OUTPUT            Output Name

  Optional Settings:
    --min=MIN          Minimum TMS Requirement
    --max=MAX          Maximum TMS Requirement
    --flank=F_LENGTH   Size of hydrophillic padding around TMSs (10 aa)
    --method=METHOD    [1] horizontal, [2] Vertical, [3] Both
    --VSrestrict=SSET  Vertical Subject Restriction.
    --VTrestrict=TSET  Vertical Target Restriction.
    --consecutive      Includes only consecutive targets 'r' TMSs apart
    --fasta_only       Build ONLY Fasta DB(s) (No TMS Searching)
    --threads=THREADS  Number of threads <default:2>

The first three settings are needed to run. To enter these parameters, enter them into the Terminal like this:

ancient -i <path to input> -r <repeat size> -o <outputname> –min=12 –max=12

without the <,>. The input file should be a FASTA formatted list of homologs. The repeat size is the size of the repeat you are looking for. A hydropathy plot of a representative protein using ‘WHAT” should give some indication of many TMSs are in the repeat. If your prediction was lower than the actual repeat size, the data generated can still reveal the true repeat size.

The output parameter is the name of the folder Ancient will generate that will contain your results.

It is recommended that you also specify the –min & –max value. In almost all cases, these should be the same number. A list of homologs typically have a handful of sequences that differ in their TMS numbers. This can result in false positives. For example, if you are using a sample population from MFS, you should set your –min & –max both to 12 (most members of the MFS have 12 TMSs).

After you have formatted your command, hit Enter & let the program run.

This could take up to several hours, depending on how large your sample size was. However, you can still view results in realtime as they are generated. Just open the output folder to view results.

The horizontal.txt file will contain horizontal searches. This means, it will show TMSs compared within the same protein. The vertical folder will have results for all internal repeats across a list of homologs.