<commit_before># Documentation for script: _matchDomains.pl_


## Summary
This program scans protein sequences against a database domain profiles (i.e.,
cog, cdd, pfam, and tigrfam) using either of [_hmmscan_](http://hmmer.org/), 
[_rpsblast_](https://www.perl.org/), or [_mmseqs_](https://github.com/soedinglab/MMseqs2).

## Contributor
<NAME>

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

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

2. **_Blast+ 2.6.0 to 2.10.0_**  
Other versions of blast may require minor adaptations. Visit the
[download site](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download). 

3. **_HHMER 3.2.1_**  
You can download this suite of programs from its [official site](http://hmmer.org/). 

4. **_MMseqs_**  
Open-source software suite for very fast, parallelized protein sequence searches
and clustering of huge protein sequence data sets. For more information, visit the
[official repository](https://github.com/soedinglab/MMseqs2).




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

 SYNOPSIS
     matchDomains.pl -q [fastaFile] -f [cog|cdd|pfam|tigrfam] [options]

 EXAMPLE
     matchDomains.pl -q GCF_000005845.faa.gz -f pfam -p mmseqs -o PFAM

     matchDomains.pl -q fastaFiles/*.faa.gz -f cdd -o CDD

 OPTIONS
     -q  query fasta file(s), required

     -f  domain database: file or [cog|cdd|pfam|tigrfam], required

     -p  program [hmmscan|rpsblast|mmseqs], except for mmseqs, can be guessed
         from database:

         -   rpsblast for cog and cdd

         -   hmmscan for Pfam and TIGRFAM

         -   mmseqs has to be specified in command line

     -o  output folder, default: scanDomains

     -e  e-value threshold, default 0.001 (NCBI uses 0.01), scientific notation
         acceptable (e.g. 1e-3)

     -x  number of CPUs to use, default: 1 (max: 4)

     -c  running in computer cluster [T|F], default 'F'<commit_msg>Update matchDomains.md<commit_after># Documentation for script: _matchDomains.pl_


## Summary
This program scans protein sequences against a database domain profiles (i.e.,
cog, cdd, pfam, and tigrfam) using either of [_hmmscan_](http://hmmer.org/), 
[_rpsblast_](https://www.perl.org/), or [_mmseqs_](https://github.com/soedinglab/MMseqs2).


## Contributor
<NAME>


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

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

2. **_Blast+ 2.6.0 to 2.10.0_**  
Other versions of blast may require minor adaptations. Visit the
[download site](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download). 

3. **_HHMER 3.2.1_**  
You can download this suite of programs from its [official site](http://hmmer.org/). 

4. **_MMseqs_**  
Open-source software suite for very fast, parallelized protein sequence searches
and clustering of huge protein sequence data sets. For more information, visit the
[official repository](https://github.com/soedinglab/MMseqs2).

5. **_Domain profile databases_**  
Download following profile databases _Pfam_, _CDD_, _COG_, and _tigrfam_ as they 
need to be locally available.


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

 SYNOPSIS
     matchDomains.pl -q [fastaFile] -f [cog|cdd|pfam|tigrfam] [options]

 EXAMPLE
     matchDomains.pl -q GCF_000005845.faa.gz -f pfam -p mmseqs -o PFAM

     matchDomains.pl -q fastaFiles/*.faa.gz -f cdd -o CDD

 OPTIONS
     -q  query fasta file(s), required

     -f  domain database: file or [cog|cdd|pfam|tigrfam], required

     -p  program [hmmscan|rpsblast|mmseqs], except for mmseqs, can be guessed
         from database:
         -   rpsblast for cog and cdd
         -   hmmscan for Pfam and TIGRFAM
         -   mmseqs has to be specified in command line

     -o  output folder, default: scanDomains

     -e  e-value threshold, default 0.001 (NCBI uses 0.01), scientific notation
         acceptable (e.g. 1e-3)

     -x  number of CPUs to use, default: 1 (max: 4)

     -c  running in computer cluster [T|F], default 'F'
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{'dir': 'git-commits-cleaned', 'id': '479192', 'n_tokens_mistral': 1570, 'n_tokens_neox': 1432, 'n_words': 512}