AGA computes the optimal pairwise alignment of a nucleic acid sequence against a reference genome, taking into account all CDS annotations of the reference to simultaneously score nucleic acid and amino acid similarity, minimize frameshifts, and avoid codon misaligned gaps.
It outputs the optimal nucleic acid sequence alignment and all CDS and protein amino acid sequence alignments.
A web version is available at http://www.genomedetective.com/app/aga
To compile AGA from source, you need a standard-compliant C++11 compiler, and CMake.
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ../
make
As input, AGA requires a reference genome and a query sequence.
The reference genome is provided as a GENBANK flatfile record. For example, go to https://www.ncbi.nlm.nih.gov/nuccore/NC_001802.1, choose Send to:, File, Format Genbank.
The query sequence is provided in a FASTA file.
build/src/aga {OPTIONS} [REFERENCE.GB] [QUERY.FASTA] [ALIGNMENT.FASTA]
This is AGA, an Annotated Genome Aligner, (c) Emweb bvba
See http://github.com/emweb/aga/LICENSE.txt for terms of use.
OPTIONS:
--help Display this help menu
--version Display the version
Alignment mode, specify one of:
--global Global alignment
--local Local alignment
Nucleic Acid Score options
--nt-weight=[WEIGHT] Weight for NT score fraction
(default=1)
--nt-gap-open=[COST] Nucleotide Gap Open penalty
(default=-10)
--nt-gap-extend=[COST] Nucleotide Gap Extension penalty
(default=-1)
--nt-match=[SCORE] Score for a nucleotide match
(default=2)
--nt-mismatch=[COST] Penalty for a nucleotide mismatch
(default=-2)
Amino Acid Score options
--aa-weight=[WEIGHT] Total weight for AA score fraction
(default=1)
--aa-gap-open=[COST] Amino Acid Gap Open penalty
(default=-6)
--aa-gap-extend=[COST] Amino Acid Gap Extension penalty
(default=-2)
--aa-matrix=[MATRIX] Substitution matrix for amino acid
matches: BLOSUM62 or BLOSUM30
(default=BLOSUM30)
--aa-frameshift=[COST] Frameshift penalty (default=-100)
--aa-misalign=[COST] Codon misalignment penalty
(default=-20)
General alignment options
--strict-codon-boundaries Do not optimize at codon boundaries
Amino acid alignments output
--cds-aa-alignments=[ALIGNMENT.FASTA]
Amino acid alignments output file of
CDS (FASTA)
--cds-nt-alignments=[ALIGNMENT.FASTA]
Nucleic acid CDS alignments output
file of CDS (FASTA)
--protein-aa-alignments=[ALIGNMENT.FASTA]
Amino acid alignments output file of
Protein Products (FASTA)
--protein-nt-alignments=[ALIGNMENT.FASTA]
Nucleic acid CDS alignments output
file of Protein Products (FASTA)
REFERENCE.GB Annotated reference (Genbank Record)
QUERY.FASTA FASTA file with nucleic acid query
sequence
ALIGNMENT.FASTA Nucleic acid alignment output file
(FASTA)
"--" can be used to terminate flag options and force all following
arguments to be treated as positional options
AGA will compute the optimal pairwise alignment of a nucleic acid query
sequence (QUERY.FASTA) against a reference genome (REFERENCE.GB), taking
into account CDS annotations in the genbank record to include in the
alignment score all amino acid alignments and minimizing frameshifts within
these open reading frames. It writes the resulting alignment to
ALIGNMENT.FASTA
aga --global NC_001802.gb query.fasta alignment.fasta
This project is licensed under the Emweb Non-Commercial Public License. See the LICENSE.txt file for details.
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