View source for PALADIN

[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
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|{{#vardefine:url|https://github.com/twestbrookunh/paladin}}
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Protein ALignment And Detection INterface

PALADIN is a protein sequence alignment tool designed for the accurate functional characterization of metagenomes.

PALADIN is based on BWA, and aligns sequences via read-mapping using BWT. PALADIN, however, offers the novel approach of aligning in the protein space. During the index phase, it processes the reference genome's nucleotide sequences and GTF/GFF annotation containing CDS entries, first converting these transcripts into the corresponding protein sequences, then creating the BWT and suffix array from these proteins. The process of translatation is skiped when providing a protein reference file (e.g., UniProt) for mapping. During the alignment phase, it attempts to find ORFs in the read sequences, then converts these to protein sequences, and aligns to the reference protein sequences.

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{{#if: {{#var: exe}}|==Additional Information==

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{{#if: {{#var: policy}}|==Usage Policy==

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{{#if: {{#var: faq}}|==FAQ==
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{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:

https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btx021/2964789/PALADIN-protein-alignment-for-functional-profiling

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{{#if: {{#var: installation}}|==Installation==
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