POA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool POA

Tool usage distribution map

This map represents all the scientific publications referring to POA per scientific context
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Associated diseases

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POA specifications


Unique identifier OMICS_14254
Name POA
Alternative name Partial Order Alignment
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A set of sequences
Input format FASTA
Output data A tabular form of the alignment in the standard PIR or CLUSTAL alignment format, or the PO-MSA representation
Output format TXT
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes




No version available


  • person_outline Christopher Lee

Additional information

POA is implemented in SPOA (SIMD partial order alignment) at: https://github.com/rvaser/spoa

Publication for Partial Order Alignment

POA citations


Preoptic leptin signaling modulates energy balance independent of body temperature regulation

PMCID: 5953538
PMID: 29761783
DOI: 10.7554/eLife.33505.023
call_split See protocol

[…] 3-month-old Leprflox/flox mice were injected with AAV-Cre:GFP (6 males and 10 females) or AAV-GFP (6 males and nine females) in the POA. Food was switched from regular chow to high fat diet (58 kcal% fat, D12331, Research Diets) right after viral injections. Weekly body weight and food intake were measured from week −3 to week 15. […]


The long reads ahead: de novo genome assembly using the MinION

PMCID: 5770995
PMID: 29375809
DOI: 10.5256/f1000research.12992.r24090

[…] lly v0.7.0 and up) were reported by its authors to work much faster. Racon Racon corrects MinION assemblies by finding a consensus sequence between reads and the assembly through the construction of partial order alignment (POA) graphs. After alignment of the reads by a mapper of choice (e.g. Minimap or Graphmap), Racon segments the sequence and finds the best alignment between a POA graph of the […]


Rapid de novo assembly of the European eel genome from nanopore sequencing reads

Sci Rep
PMCID: 5543108
PMID: 28775309
DOI: 10.1038/s41598-017-07650-6

[…] irst corrected nanopore-derived scaffolds with nanopore data using Racon, based on alignments produced by Graphmap version 0.3.0. Ultimately Racon sequence correction is performed by SPOA, which is a partial order alignment algorithm that generates consensus sequences.Subsequently, we used previously generated Illumina data (NCBI Sequence Read Archive SRR5235521– SRR5235523), trimmed to Phred 30 q […]


Population and allelic variation of A to I RNA editing in human transcriptomes

Genome Biol
PMCID: 5532815
PMID: 28754146
DOI: 10.1186/s13059-017-1270-7
call_split See protocol

[…] For the multiple sequence alignment of the Alu sequences, we used POA (Partial Order Alignment) []. Alu sequences on each end of the IRAlu hairpin were aligned separately to avoid misalignments across Alu sequences. A white spacer region was placed between the two A […]


Nanopore long read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

Nat Commun
PMCID: 5524981
PMID: 28722025
DOI: 10.1038/ncomms16027

[…] ive splice sites it contained. Isoforms that contained at least 1% of all reads at a gene locus were retained. All the reads in these retained isoform groups were used to create consensus reads using POA. In short, fasta files containing all read sequence are passed to POA, which generates a consensus of the reads by creating a multiple sequence alignment of the reads in the form of a partially or […]


Rapid resistome mapping using nanopore sequencing

Nucleic Acids Res
PMCID: 5416750
PMID: 28062856
DOI: 10.1093/nar/gkw1328

[…] rect has been applied previously to increase the nanopore read accuracy from 80.5% to 95.9% (). The algorithm identifies overlapping reads using DALIGNER () and calculates a consensus sequence, using partial-order alignment (POA) software (). Two rounds of error correction where conducted by the poreFUME pipeline. Finally, the error corrected reads were polished using nanopolish () which uses the […]

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POA institution(s)
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
POA funding source(s)
This work was supported by Department of Energy grant DEFG0387ER60615, National Science Foundation grant IIS-0082964, a grant from the Searle Scholars Program, and by a Department of Energy Computational Science Graduate fellowship.

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