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Protocols

PerM specifications

Information


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

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Documentation


Publication for Periodic Seed Mapping

PerM citations

 (5)
call_split

Effect of RNA integrity on uniquely mapped reads in RNA Seq

2014
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 […]

library_books

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

2014
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 […]

library_books

A hybrid short read mapping accelerator

2013
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 […]

library_books

Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows

2012
Genes
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- […]

library_books

Seeds for effective oligonucleotide design

2011
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 […]

Citations

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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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