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Protocols

IMEx specifications

Information


Unique identifier OMICS_04100
Name IMEx
Alternative name Imperfect Microsatellite Extractor
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Perl
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Hampapathalu A. garajaram

Information


Unique identifier OMICS_04100
Name IMEx
Alternative name Imperfect Microsatellite Extractor
Interface Web user interface
Restrictions to use None
Programming languages C, Perl
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Hampapathalu A. garajaram

Publication for Imperfect Microsatellite Extractor

IMEx citations

 (9)
library_books

Genome sequencing and analysis of Alcaligenes faecalis subsp. phenolicus MB207

2018
Sci Rep
PMCID: 5827749
PMID: 29483539
DOI: 10.1038/s41598-018-21919-4

[…] chosen cut-off values, specified per gene cluster type and genes represented in specified colours referring to certain functionality., ssr and cssr information was extracted using the software imex in batch, using the parameters: include flanking regions: 10 bp, type of repeat: imperfect; repeat size: all; minimum repeat number: mono: 12, di: 6, tri: 4, tetra: 3, penta: 3, hexa: 3, […]

library_books

Using genomic data to develop chloroplast DNA SSRs for the Neotropical liana Stizophyllum riparium (Bignonieae, Bignoniaceae)1

2017
Appl Plant Sci
PMCID: 5664965
PMID: 29109920
DOI: 10.3732/apps.1700061

[…] the chloroplast genome for s. riparium was annotated using dogma (dual organellar genome annotator; ; http://dogma.ccbb.utexas.edu/). start and stop codons were inspected and adjusted manually., the imperfect microsatellite extractor (imex) interface () was used to detect perfect microsatellites, with a threshold of 10 repeat units for mononucleotide and six repeats for di-, tri-, tetra-, […]

library_books

Complete Chloroplast Genome Sequences and Comparative Analysis of Chenopodium quinoa and C. album

2017
Front Plant Sci
PMCID: 5635682
PMID: 29056940
DOI: 10.3389/fpls.2017.01696

[…] to 2, 7, 7, respectively; the minimum alignment score to report repeats was 50; the minimum length was 6 bp; and the motif identity percent was 100%. the simple sequence repeats were detected using imex (www.mcr.org.in/imex; mudunuri and nagarajaram, ) with minimal repeat numbers of 10, 5, 4, 3, 3, and 3 for mono-, di-, tri-, tetra-, penta-, and hexa-nucleotides, respectively. the substitution […]

library_books

Database of Periodic DNA Regions in Major Genomes

2017
Biomed Res Int
PMCID: 5274682
PMID: 28182099
DOI: 10.1155/2017/7949287

[…] pairwise similarity, these approaches are unable to find the latent periodicity. first of all, it involves algorithms and programs, such as trf [], mreps [], trstalker [], atrhunter [], t-reks [], imex [, ], crisprs [], swan [], and some others [, ], because similarity between the different periods is very low in case of latent periodicity. this leads to the lack of seeds and identical short […]

call_split

A genomic approach for isolating chloroplast microsatellite markers for Pachyptera kerere (Bignoniaceae)1

2016
Appl Plant Sci
PMCID: 5033366
PMID: 27672522
DOI: 10.3732/apps.1600055
call_split See protocol

[…] genome for p. kerere was annotated using the software geneious version 4.7.5 (biomatters ltd., auckland, new zealand). start and stop codons were inspected and adjusted manually., we used the imperfect microsatellite extractor (imex) interface () to detect perfect and imperfect microsatellites, with minimum thresholds of four repeat units for tri-, tetra-, penta-, and hexa-; six for di-; […]

library_books

Microsatellite markers for Senna spectabilis var. excelsa (Caesalpinioideae, Fabaceae)1

2016
Appl Plant Sci
PMCID: 4716775
PMID: 26819856
DOI: 10.3732/apps.1500062

[…] são paulo, brazil). identification of simple sequence repeats was performed with the software ssrit (simple sequence repeat identification tool; http://archive.gramene.org/db/markers/ssrtool) and imperfect microsatellite extractor (). primer design was done using the software primer3plus () with the following criteria: product size range 100–300 bp, primer melting temperature (tm) 50–60°c […]


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IMEx institution(s)
Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad, India
IMEx funding source(s)
Supported by the Department of Biotechnology (DBT) India.

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