RfamConcealer

Overview

RfamConcealer is a Java program that selects and processes random (sub)sequences from a reference database, specifically focusing on RFAM families. The tool can generate MAF files, realign sequences using MAFFT, and produce Clustal files for multiple sequence alignments.

Features

• Data Loading and Preparation: Load and prepare sequences from FASTA files in the specified input directory.
• Sequence Sampling: Sample sequences from each RFAM family based on specified parameters.
• MAFFT Realignment: Realign sequences using MAFFT and save the results in MAF format.
• Clustal File Generation: Generate Clustal files for multiple sequence alignment.

Requirements

• Java 8 or higher
• MAFFT installed (with the mafft-ginsi executable available)
• A directory containing FASTA files as the input database

Usage

You can run the RfamConcealer program from the command line using the following syntax: 'java RfamConcealer [options] -i [path to .fasta database folder]'

• -i <string>: (Required) Specifies the path to the directory containing the FASTA files.
• -v: Enables verbose output for detailed logging during execution.
• -min_pi <int>: Sets the minimum pairwise identity percentage (default: 10).
• -max_pi <int>: Sets the maximum pairwise identity percentage (default: 80).
• -max_f <int>: Sets the maximum number of sequences per RFAM family/input file (default: 20).
• -min_f <int>: Sets the minimum number of sequences per RFAM family/input file (default: 2).
• -t <int>: Sets the maximum total number of sequences to include (default: 200).
• -o <string>: Specifies the output directory where the results will be saved (default: ./rfam_subset.fa).

Output

Upon successful execution, the program generates the following output:

• MAF File:

  • Location: The MAF file is saved in the output directory specified by the -o option (default: ./rfam_subset.fa/output.maf).
  • Description: Contains realigned sequences in MAF format, including information on pairwise identities.

• Clustal Files:

  • Location: Stored in a ClustalFiles subdirectory within the specified output directory.
  • Description: Clustal format files generated for each RFAM family, useful for multiple sequence alignments.

• Log Information:

  • Description: If the -v (verbose) option is enabled, detailed logs about the processing steps are printed to the console, including sequence sampling and alignment information.