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ParaAT 2.0

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ParaAT (Parallel Alignment and back-Translation, ) is a parallel tool that constructs protein-coding DNA alignments for a large number of homologs. ParaAT is well suited for large-scale data analysis in the high-throughput era, providing good scalability and exhibiting high parallel efficiency for computationally demanding tasks.

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You will need 3 files: a file of homolog clusters, a fasta file of corresponding nucleotide coding sequences, and a fasta file of corresponding peptide sequences.  For the homolog file, ParaAT accepts a tab-delimited text file with each row representing a homologous group. For testing, and for an example of the format for the homolog file, see Community Data -> iplantcollaborative -> example_data -> paraat -> input

Example format for homolog file:

NP_000005 NP_783327 XP_001139819

 NP_000006 NP_032699 XP_001146758

NP_000008 NP_031409 XP_001162935
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An additional file that specifies the number of processors to be used is provided in the Discovery Environment along with example data.

Parameters Used in App

1. Multiple Aligner - Select from options within App (tcoffee, mafft, muscle, clustalw2)
2. Output Format - Select from options within App (fasta, codon, axt, clustal, paml)
3. Genetic Code - enter the number for the desired option from the list below.  The Standard Code is the default.
   • 1. The Standard Code
   • 2. The Vertebrate Mitochondrial Code
   • 3. The Yeast Mitochondrial Code
   • 4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
   • 5. The Invertebrate Mitochondrial Code
   • 6. The Ciliate, Dasycladacean and Hexamita Nuclear Code
   • 9. The Echinoderm and Flatworm Mitochondrial Code
   • 10. The Euplotid Nuclear Code
   • 11. The Bacterial, Archaeal and Plant Plastid Code
   • 12. The Alternative Yeast Nuclear Code
   • 13. The Ascidian Mitochondrial Code
   • 14. The Alternative Flatworm Mitochondrial Code
   • 16. Chlorophycean Mitochondrial Code
   • 21. Trematode Mitochondrial Code
   • 22. Scenedesmus obliquus Mitochondrial Code
   • 23. Thraustochytrium Mitochondrial Code
   • 24. Pterobranchia Mitochondrial Code
   • 25. Candidate Division SR1 and Gracilibacteria Code
4. Remove Aligned Codons with Gaps - select if you want ParaAT to remove from the output.
5. Remove Mismatched Codons - select if you want ParaAT to remove these from the output.

Output File(s)

There are 5 output format options:  axt, fasta, paml, codon, and clustal.  By default, ParaAT is set to create output files according to its 'verbose' parameter.  Multiple files will be output for each homolog cluster that was successfully processed. cluster.cds_aln.fasta is the primary output file.

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