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Conventional primer design Microsatellite detection

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palfinder specifications

Desktop

Information

Unique identifier	OMICS_00111
Name	palfinder
Software type	Application/Script
Interface	Command line interface
Restrictions to use	None
Biological technology	Illumina, Roche
Operating system	Unix/Linux, Mac OS
Programming languages	Perl
License	GNU General Public License version 2.0
Computer skills	Advanced
Version	0.02.04
Stability	Stable
Maintained	Yes

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palfinder citations

(3)

Development of microsatellite loci of pod mahogany, Afzelia quanzensis (Fabaceae), by Illumina shotgun sequencing, and cross amplification in A. africana1

2016

Appl Plant Sci

PMCID: 4915920

PMID: 27347453

DOI: 10.3732/apps.1600010

[…] encer (Illumina, San Diego, California, USA).The resulting raw Illumina paired-end sequencing reads were analyzed with a Perl script, PAL_FINDER_v0.02.04 (available at http://sourceforge.net/projects/palfinder), which identifies microsatellite loci without the need for prior sequence trimming and assembly (). The Perl script was run with Primer3 version 2.0.0 () for simultaneous primer design. Def […]

Microsatellite loci discovery from next generation sequencing data and loci characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758)

2016

PeerJ

PMCID: 4878368

PMID: 27231653

DOI: 10.7717/peerj.2019

See protocol

[…] ity-checked paired-end reads with FastQC (). The software FastqMcf was used to trim adapters, cut low quality ends and remove low quality reads and their mate-pair read ().We executed the perl script palfinder to identify short sequence repeat regions (). The script also calls Primer3, version 2.0.0, to identify potential primer pairs that span the repeat region (). The minimum number of repeat un […]

Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae)

2015

PLoS One

PMCID: 4641700

PMID: 26561396

DOI: 10.1371/journal.pone.0142602

[…] A variety of software is available to identify microsatellites in NGS datasets (MISA, palfinder, MSATCOMMANDER, QDD), and all of these can effectively process data from 454 and Illumina platforms. QDD is an open acess program, and among the most user-friendly and versatile of the softw […]

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