<commit_before># Documentation for script: _tmsRepeat.pl_

## Summary
We developed tmsRepeat as a strategy to identify repeated regions of TMSs in a 
transporter sequence that allows incorporation of prior knowledge about 
the TMS topology and expected size of the repeat unit. The program cuts TMS-bundles 
of a specified length depending on the size of the repeat unit expected by the user, 
aligns the sequences of the different TMS- bundles with the Smith-Waterman algorithm, 
prints the results in a HTML report that includes the hydropathy plots of the proteins 
in a family, the limits of the bundles aligned and shows what regions within the bundles 
were contained in the alignments.


## How to cite this program
If you find this program useful, please cite the paper:  

  * <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>. 
  _Bioinformatic characterization of the Anoctamin Superfamily of Ca2+-activated ion 
  channels and lipid scramblases._  2018. PLoS One. **13**(3):e0192851 
  **PMID:** [29579047](https://www.ncbi.nlm.nih.gov/pubmed/?term=29579047)  


## Dependencies
The following programs need to be available in your path for this 
program to run properly:

1. **_ssearch36 version: 36.3.8e_**  
Other versions of ssearch may require minor adaptations. Visit the
[download site](https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml). 

2. **_tmsplit_**  
This program is available in our [Python repository](https://github.com/SaierLaboratory/BioVx).

3. **_extractFamily.pl_**  
This program is available in our [Perl repository](https://github.com/SaierLaboratory/TCDBtools). 

4. **_quod.py_**  
This program is available in our [Python repository](https://github.com/SaierLaboratory/BioVx).

5. **_PERL 5.18_**  
Visit the [official website](https://www.perl.org/). This program 
was not tested with more recent versions of perl.

## Command line options
The following options are available. You can also run the 
script without arguments to display the options:

    -i, --infile {path}
      Input file with id/accession(s) of the protein(s) to analyze and the coordinates
      of the TMSs in that protein(s).
      (Argument is mandatory).

    -s, --seqs {path}
      Directory to access the sequences in FASTA format that will be used to 
      search for repeats.
      (Argument is mandatory)

    -f, --id-format {string}
      Format of identifier used:
        tc    plain tcdb identifier of a system (e.g., 2.A.1.8.1)
        tca   tcdb id and accession separated by dash (e.g. 2.A.1.8.3-Q9R6U5)
        o     other, it can be refSeq, uniprot or custom, but it is requried
              that is is a single string without spaces.
      (Argument is mandatory)

    -r, --repeat-unit {int)
      Expected size in TMS of the repeat unit to search in the protein.
      (Argument is mandatory)

    -t, --tail-size {int}
      Number of residues to add to the beginning and end of TMS regions before
      running comparisons. Value should be less than or equal to 15 residues.
     (Default: 5);

    -e, --evalue {float}
      Maximum evalue to consider an alignment between two TMS bundles significant.
      (Default: 0.1);

    -c, --coverage {float}
      Minimum alignment coverage of the smallest bundle to consider an alignment
      signifiant.
      (default: 0.8)

    -id, --perc-identity {float}
       Minimum identity in the alignemnt to consider alignments signficant.
       (defatul 0.3);

    -gs, --gsat-shuffles {int}
       Number of shuffles that will be used to run GSAT on good matches.
<commit_msg>Update tmsRepeat.md<commit_after># Documentation for script: _tmsRepeat.pl_

## Summary
We developed tmsRepeat as a strategy to identify repeated regions of TMSs in a 
transporter sequence that allows incorporation of prior knowledge about 
the TMS topology and expected size of the repeat unit. The program cuts TMS-bundles 
of a specified length depending on the size of the repeat unit expected by the user, 
aligns the sequences of the different TMS- bundles with the Smith-Waterman algorithm, 
prints the results in a HTML report that includes the hydropathy plots of the proteins 
in a family, the limits of the bundles aligned and shows what regions within the bundles 
were contained in the alignments.


## How to cite this program
If you find this program useful, please cite the paper:  

  * <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME> Jr. 
  _Bioinformatic characterization of the Anoctamin Superfamily of Ca2+-activated ion 
  channels and lipid scramblases._  2018. PLoS One. **13**(3):e0192851 
  **PMID:** [29579047](https://www.ncbi.nlm.nih.gov/pubmed/?term=29579047)  


## Dependencies
The following programs need to be available in your path for this 
program to run properly:

1. **_ssearch36 version: 36.3.8e_**  
Other versions of ssearch may require minor adaptations. Visit the
[download site](https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml). 

2. **_tmsplit_**  
This program is available in our [Python repository](https://github.com/SaierLaboratory/BioVx).

3. **_extractFamily.pl_**  
This program is available in our [Perl repository](https://github.com/SaierLaboratory/TCDBtools). 

4. **_quod.py_**  
This program is available in our [Python repository](https://github.com/SaierLaboratory/BioVx).

5. **_PERL 5.18_**  
Visit the [official website](https://www.perl.org/). This program 
was not tested with more recent versions of perl.

## Command line options
The following options are available. You can also run the 
script without arguments to display the options:

    -i, --infile {path}
      Input file with id/accession(s) of the protein(s) to analyze and the coordinates
      of the TMSs in that protein(s). Use option -if to specify the format of this
      file. (Argument is mandatory).
      
    -if, --infile-format {string} (optional)
      Format of the TMS coordenates. It can be either 'tms' or 'hmmtop'.
      (Default: hmmtop)

    -o, --outdir {path}
      Output directory where results will be saved.
      (Default: repeats)
      
    -s, --seqs {path}
      Directory to access the sequences in FASTA format that will be used to 
      search for repeats. One file per sequence, and the name of the file is
      the accession of the protein followed by '.faa'
      (Argument is mandatory)

    -f, --id-format {string}
      Format of identifier used:
        tc    plain tcdb identifier of a system (e.g., 2.A.1.8.1)
        tca   tcdb id and accession separated by dash (e.g. 2.A.1.8.3-Q9R6U5)
        o     other, it can be refSeq, uniprot or custom, but it is requried
              that is is a single string without spaces.
      (Argument is mandatory)

    -r, --repeat-unit {int)
      Expected size in TMS of the repeat unit to search in the protein.
      (Argument is mandatory)

    -t, --tail-size {int}
      Number of residues to add to the beginning and end of TMS regions before
      running comparisons. Value should be less than or equal to 15 residues.
     (Default: 5)

    -e, --evalue {float}
      Maximum evalue to consider an alignment between two TMS bundles significant.
      (Default: 0.1)

    -cs, --comp-stats {FLAG}
      If present, this flag indicates that  E-values will be corrected using
      compositional statistics.  (Default: not corrected)

    -c, --coverage {float}
      Minimum alignment coverage of the smallest bundle to consider an alignment
      signifiant.  (Default: 0.8)

    -id, --perc-identity {float}
       Minimum identity in the alignemnt to consider alignments signficant.
       (defatul 0.3);

    -gs, --gsat-shuffles {int}
      Number of shuffles that will be used to run GSAT on good matches.
       
    -z, --gsat-cutoff {int}
      Minimum GSAT score cutoff to select good hits. 
      (Default: 4.0)

    -h, --help
      Print this help message. It takes precedence to any other option.       
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