Dotlet protocols

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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 in pipelines

 (3)
2017
PMCID: 5555486
PMID: 28659292
DOI: 10.1534/g3.117.042093

[…] from the number of reads present in each cluster divided by the total number of reads. we searched for clusters with high graph density, which is a typical characteristic of satdnas families (). the dotlet software () was also used to generate a scrutinized description of full length copies of each satdna family., multiple satdna sequences were aligned with the muscle algorithm () […]

2017
PMCID: 5737874
PMID: 28854689
DOI: 10.1093/dnares/dsx010

[…] were carefully analysed through dot plots to determine the start and end of each repeat. dot plots were also used to check for similarity between marmosat and as. these plots were generated with the dotlet application with a 15 bp word size and 60% similarity cutoff., multiple sequence alignments were performed using muscle 4.0. the mega software version 5.05 was used for the calculation […]

2010
PMCID: 3091767
PMID: 21080964
DOI: 10.1186/1471-2164-11-637

[…] [], rendered with jalview [] and manually annotated. protein domains in candidate virulence genes were identified using pfam []. identity dotplots for repeat containing proteins were drawn using dotlet with word size of 7 [], motifs were found using meme []., whole genome expression data used in this work were previously described by haas et al. [] and are based on a custom nimblegen […]

Dotlet in publications

 (17)
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 […]

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 […]

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 […]

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 […]

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 () […]

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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