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Dotlet specifications

Information


Unique identifier OMICS_15826
Name Dotlet
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Javascript
License GNU Affero General Public License version 3
Computer skills Medium
Version 1.5
Stability No
Maintained No

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Maintainer


This tool is not maintained anymore.

Additional information


https://myhits.isb-sib.ch/util/dotlet/doc/dotlet_help.html

Information


Unique identifier OMICS_15826
Name Dotlet
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 0.1.1
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Thomas Junier

Additional information


https://myhits.isb-sib.ch/util/dotlet/doc/dotlet_help.html

Publication for Dotlet

Dotlet citations

 (18)
library_books

New insights into the genome repetitive fraction of the Antarctic bivalve Adamussium colbecki

2018
PLoS One
PMCID: 5874043
PMID: 29590185
DOI: 10.1371/journal.pone.0194502

[…] features related to transposable elements were searched in repbase using censor (http://www.girinst.org/censor/) []. the detection of internal repeats was performed through dotlet (http://myhits.isb-sib.ch/cgi-bin/dotlet) [], while trnascan-se search server (http://lowelab.ucsc.edu/trnascan-se/) [,] was used to search for motifs corresponding to the internal promoters […]

library_books

Functional and Expression Analyses of the Pneumocystis MAT Genes Suggest Obligate Sexuality through Primary Homothallism within Host Lungs

2018
MBio
PMCID: 5821091
PMID: 29463658
DOI: 10.1128/mBio.02201-17

[…] based on inversion of the loci (). we extensively compared the regions flanking the pneumocystis mat genes to each other with the help of local and global alignment tools (), as well as that of dotlet for visual appraisal of the distribution of local similarity (). no such cis-acting sequences were identified within the three pneumocystis genomes. this observation further suggested […]

library_books

Uncovering the evolutionary history of neo XY sex chromosomes in the grasshopper Ronderosia bergii (Orthoptera, Melanoplinae) through satellite DNA analysis

2018
BMC Evol Biol
PMCID: 5767042
PMID: 29329524
DOI: 10.1186/s12862-017-1113-x

[…] of 50 for minimum alignment was considered for reporting. to confirm the tandem organization and to identify monomers of the same family, we used the dotplot graphic alignment tool implemented in dotlet []. to identify a representative copy of a given satdna family, the monomers with maximum length was taken. to check similarity with published sequences, monomers were used as the query […]

library_books

Satellite DNAs are conserved and differentially transcribed among Gryllus cricket species

2017
PMCID: 5909420
PMID: 29096008
DOI: 10.1093/dnares/dsx044

[…] we examined those clusters that displayed repeat graph density in the repeatexplorer summary output to identify satdnas families. we refined the identification using dotplot graphics implemented in dotlet to confirm their tandem organization. all clusters containing reads with sequences represented above 0.01% of genome proportion (high copy number sequences) were analysed in detail., clusters […]

library_books

A Horizontally Transferred Autonomous Helitron Became a Full Polydnavirus Segment in Cotesia vestalis

2017
PMCID: 5714489
PMID: 29042411
DOI: 10.1534/g3.117.300280

[…] pdv genomes, and other pdv-related sequences, available in genbank (). to detect structural features on the pdv-like sequences found in the selected contig, we first used dotplots from the software dotlet (), followed by manual curation of sequences. finally, the analysis of palindromic or inverted repeat motifs, and their predicted secondary structures, were made using the software mfold () […]

library_books

High throughput analysis of the satellitome revealed enormous diversity of satellite DNAs in the neo Y chromosome of the cricket Eneoptera surinamensis

2017
Sci Rep
PMCID: 5527012
PMID: 28743997
DOI: 10.1038/s41598-017-06822-8

[…] for clusters that showed repeat graph density in summary output, which is a typical characteristic of satdnas families in this approach, and refined this search using dot plot charts implemented in dotlet., clusters with high graph density were submitted to the tandem repeats finder (trf) algorithm to identify the dna sequence that maximized the alignment scores between the different monomers […]


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Dotlet institution(s)
Swiss Institute of Bioinformatics, Swiss Institute for Experimental Cancer Research, Epalinges, Switzerland
Dotlet funding source(s)
Supported by grant 31-49669.96 from the Swiss National Research Foundation.

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