PALADIN: protein alignment for functional profiling whole metagenome shotgun data.
BACKGROUND
Whole metagenome shotgun sequencing is a powerful approach for assaying the functional potential of microbial communities. We currently lack tools that efficiently and accurately align DNA reads against protein references, the technique necessary for constructing a functional profile. Here, we present PALADIN-a novel modification of the Burrows-Wheeler Aligner that provides accurate alignment, robust reporting capabilities and orders-of-magnitude improved efficiency by directly mapping in protein space.


RESULTS
We compared the accuracy and efficiency of PALADIN against existing tools that employ nucleotide or protein alignment algorithms. Using simulated reads, PALADIN consistently outperformed the popular DNA read mappers BWA and NovoAlign in detected proteins, percentage of reads mapped and ontological similarity. We also compared PALADIN against four existing protein alignment tools: BLASTX, RAPSearch2, DIAMOND and Lambda, using empirically obtained reads. PALADIN yielded results seven times faster than the best performing alternative, DIAMOND and nearly 8000 times faster than BLASTX. PALADIN's accuracy was comparable to all tested solutions.


METHODS
PALADIN was implemented in C, and its source code and documentation are available at https://github.com/twestbrookunh/paladin.


BACKGROUND
anthonyw@wildcats.unh.edu.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Computer Science, University of New Hampshire, Durham, NH, USA.
Anthony
A
Westbrook
Department of Computer Science, University of New Hampshire, Durham, NH, USA.|Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA.
Jordan
J
Ramsdell
Department of Molecular Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
Taruna
T
Schuelke
Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA.
Louisa
L
Normington
Department of Computer Science, University of New Hampshire, Durham, NH, USA.|Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA.
R Daniel
RD
Bergeron
Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA.|Department of Molecular Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
W Kelley
WK
Thomas
Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA.|Department of Molecular Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
Matthew D
MD
MacManes
D000465:Algorithms; D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software