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PerM specifications


Unique identifier OMICS_00675
Name PerM
Alternative name Periodic Seed Mapping
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A reference sequence, a read as the input files.
Biological technology Illumina, Life Technologies
Operating system Unix/Linux
License Apache License version 2.0
Computer skills Advanced
Version 0.4.0
Stability Stable
Maintained Yes




No version available


Publication for Periodic Seed Mapping

PerM citations


Effect of RNA integrity on uniquely mapped reads in RNA Seq

BMC Res Notes
PMCID: 4213542
PMID: 25339126
DOI: 10.1186/1756-0500-7-753
call_split See protocol

[…] eparation kit v2 (FC-121-2001).Each DNA library was sequenced with 4.5–60 million 100 bp single-end reads on an Illumina HiSeq2000. The reads were uniquely mapped with three or fewer mismatches using PerM [] to GENCODE v17. For each protocol, we calculated Pearson’s pairwise correlation coefficients (denoted by the letter R) between the degraded and high-quality sample across the HUGO genes which […]


Evaluation and Comparison of Multiple Aligners for Next Generation Sequencing Data Analysis

Biomed Res Int
PMCID: 3980841
PMID: 24779008
DOI: 10.1155/2014/309650

[…] apping for NGS data analysis. For examples, there are Mapping and Assembly with Qualities (MAQ) developed by Li et al. [], Basic Oligonucleotide Alignment Software (BOAT) developed by Zhao et al. [], Periodic Seed Mapping (PerM) developed by Chen et al. [], Short Oligonucleotide Analysis Package (SOAPv2) developed by Li et al. [, ], and Global Alignment Short Sequence Search Software (GASSST) deve […]


A hybrid short read mapping accelerator

BMC Bioinformatics
PMCID: 3598928
PMID: 23441908
DOI: 10.1186/1471-2105-14-67

[…] the table contents utilizing on-chip memory resources, the supported reference genome size is quite limited. Tang et al. [] presented a heterogeneous short read aligner based on the algorithm used in PerM []. For its current version, the maximum working clock frequency is 175 MHz and gaps are not allowed. Olson et al. [] designed another FPGA aligner based on the BFAST algorithm. The index data st […]


Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows

PMCID: 3490498
PMID: 23139896
DOI: 10.3390/genes3030545

[…] rs dealing with highly repetitive genomic regions, it is possible to force these algorithms to output all the possible hits with a high cost in terms of speed, or to use a probabilistic software like PERM that outputs all the found hits. The user could perform a de novo assembly (see next paragraph) for a better resolution in such regions. If the main interest is the detection of CNVs with paired- […]


Seeds for effective oligonucleotide design

BMC Genomics
PMCID: 3128067
PMID: 21627845
DOI: 10.1186/1471-2164-12-280

[…] used not only by similarity search programs such as PatternHunter [], PatterHunter II [], Yass [] but also by many tools for read alignment of the next generation sequencing data, such as SHRiMP [], PerM [], SToRM []. However, there seems to be no software for oligonucleotide design that uses multiple spaced seeds. Most of them use BLAST and we found that only ProDesign [] uses a single transitio […]


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PerM institution(s)
Program in Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA, USA
PerM funding source(s)
National Institutes of Health Center of Excellence in Genomic Sciences

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