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Dotter specifications


Unique identifier OMICS_15828
Name Dotter
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data A protein or DNA sequence.
Input format FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License GNU General Public License version 3.0
Computer skills Medium
Version 4.1.5
Stability Stable
Maintained Yes


No version available


  • person_outline Richard Durbin
  • person_outline Gemma Barson

Additional information

Publications for Dotter

Dotter citations


The Xylella fastidosa RTX operons: evidence for the evolution of protein mosaics through novel genetic exchanges

BMC Genomics
PMCID: 5935956
PMID: 29728072
DOI: 10.1186/s12864-018-4731-9
call_split See protocol

[…] Seattle) and distance trees using Protdist and Fitch were determined. Protein distances were calculated using the Jones, Thornton, Taylor distance matrix []. The dotplot analysis was performed using Dotter in the ms dos environment []. […]


Structure and Distribution of Centromeric Retrotransposons at Diploid and Allotetraploid Coffea Centromeric and Pericentromeric Regions

Front Plant Sci
PMCID: 5818461
PMID: 29497436
DOI: 10.3389/fpls.2018.00175

[…] s of Coffea) sequences were identified from the NJ tree. These sequences were sub-classified into groups according to tree conformation and bootstrap values. Groups were validated by alignments using dotter (Sonnhammer and Durbin, ), stretcher (EMBOSS) and plotcon (EMBOSS). LTR sequences with 99% identity based on LTR_STRUC were annotated using Artemis (Rutherford et al., ). Complete (i.e., a LTR- […]


Simple and Complex Centromeric Satellites in Drosophila Sibling Species

PMCID: 5844345
PMID: 29305387
DOI: 10.1534/genetics.117.300620
call_split See protocol

[…] imcent2 sequences. Alignments were made using the Clustal Omega server of the European Molecular Biology Laboratory–European Bioinformatics Institute and adjusted by hand. Dot matrices were made with Dotter (). […]


Evolution of Tandem Repeat Satellite Sequences in Two Closely Related Caenorhabditis Species. Diminution of Satellites in Hermaphrodites

PMCID: 5748669
PMID: 29182550
DOI: 10.3390/genes8120351

[…] e assembly should provide a more accurate determination of tandem repeat lengths.Chromosomes and chromosome fragments of the two species were aligned with the M-GCAT program [,]. The dot-plot program DOTTER was also used for local alignments [,]. […]


Long read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline

Sci Rep
PMCID: 5696478
PMID: 29158564
DOI: 10.1038/s41598-017-16171-1

[…] te) described by Johnson et al.. To check the expected relationship between pairs of allelic sequences we inspected dotplot alignments of representative sequences (not shown) created with the program dotter. To define the small host sequence duplicated during integration, BLASTN was used to align the pre-integration site with 5′ and 3′ KoRV breakpoint sequences from the proviral sequence. For 51 s […]


Long noncoding RNAs in the model species Brachypodium distachyon

Sci Rep
PMCID: 5595811
PMID: 28900227
DOI: 10.1038/s41598-017-11206-z

[…] e CD-HIT program version 4.6 was applied to perform a cluster sequence analysis to check sequence identity between lncRNAs and ESTs with a cutoff equal to 95%. Results were further investigated using Dotter and mVISTA. […]


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Dotter institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Dotter funding source(s)
Supported by the Wellcome Trust Grant (098051); and the National Human Genome Research Institute Grant (5U54HG00455-04).

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