Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA

Bizzaro, Jeff W; Marx, Kenneth A.

doi:10.1186/1471-2105-4-22

Cited by 23 publications

(8 citation statements)

References 13 publications

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“…Correspondingly, there are several software tools intended to discover and annotate microsatellites. Some of them can identify only perfect microsatellites (SSRIT [22], Poly [23], TROLL [24], GMATo [25], GMATA [26]) while others can identify also imperfect microsatellites (TRF [27] and pSTR Finder [28], Sputnik [29], Star [30], G-IMEx [31], mreps [32], TandemSWAN [33], SciRoKo [34], Dot2Dot [35], ProGeRF [36], BWtrs [37], T-REKS [38], XSTREAM [39], SSR Locator [40]).…”

Section: Introductionmentioning

confidence: 99%

ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation

et al. 2019

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Background Mitochondria is a powerhouse of all eukaryotic cells that have its own circular DNA (mtDNA) encoding various RNAs and proteins. Somatic perturbations of mtDNA are accumulating with age thus it is of great importance to uncover the main sources of mtDNA instability. Recent analyses demonstrated that somatic mtDNA deletions depend on imperfect repeats of various nature between distant mtDNA segments. However, till now there are no comprehensive databases annotating all types of imperfect repeats in numerous species with sequenced complete mitochondrial genome as well as there are no algorithms capable to call all types of imperfect repeats in circular mtDNA. Results We implemented naïve algorithm of pattern recognition by analogy to standard dot-plot construction procedures allowing us to find both perfect and imperfect repeats of four main types: direct, inverted, mirror and complementary. Our algorithm is adapted to specific characteristics of mtDNA such as circularity and an excess of short repeats - it calls imperfect repeats starting from the length of 10 b.p. We constructed interactive web available database ImtRDB depositing perfect and imperfect repeats positions in mtDNAs of more than 3500 Vertebrate species. Additional tools, such as visualization of repeats within a genome, comparison of repeat densities among different genomes and a possibility to download all results make this database useful for many biologists. Our first analyses of the database demonstrated that mtDNA imperfect repeats (i) are usually short; (ii) associated with unfolded DNA structures; (iii) four types of repeats positively correlate with each other forming two equivalent pairs: direct and mirror versus inverted and complementary, with identical nucleotide content and similar distribution between species; (iv) abundance of repeats is negatively associated with GC content; (v) dinucleotides GC versus CG are overrepresented on light chain of mtDNA covered by repeats. Conclusions ImtRDB is available at http://bioinfodbs.kantiana.ru/ImtRDB/ . It is accompanied by the software calling all types of interspersed repeats with different level of degeneracy in circular DNA. This database and software can become a very useful tool in various areas of mitochondrial and chloroplast DNA research.

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Section: Introductionmentioning

confidence: 99%

ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation

et al. 2019

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“…In each case, flanking sequences were obtained up to a maximum length (correlating to the median size of the IGR as indicated in Additional file 1 : Table S1) unless the adjacent ORF was encountered, in which case, only the flanking sequence up to the ORF was taken. The open source algorithm Poly (see Methods) was used to search for and provide quantitative data on the frequencies of homopolymer tracts nucleotides A, G, C and T (collectively termed i) for all lengths N [ 3 , 34 ]. These data include: (1) the fraction of each nucleotide i within these sequences (Fraction i ), (2) the frequency of each tract i of length N bases observed ( f i N obs) as well as that expected ( f i N exp) from randomized sequences of the same length and nucleotide content, (3) the maximal length of each homopolymer tract observed (N max obs, where the occurrence of N max obs was ≥ 4) and that expected (N max exp), again, from randomized sequences of the same length and nucleotide content (Figure 2 and Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

“…The ends of each individual flanking sequence were tagged to prevent the joining of sequences that may create a homopolymeric tract artefact between two sequences. Individual files were analysed using the program Poly [ 34 ], open source software publically available from http://www.bioinformatics.org/poly . Non-overlapping homopolymer tracts of all four types are counted by Poly for the entire file and a number of parameters are then calculated, including: the total base count for each file, its GC composition, and the numbers and the frequencies of the homopolymer tracts of different lengths.…”

Section: Methodsmentioning

confidence: 99%

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Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites

Russell

Cheng

Bizzaro³

et al. 2014

BMC Genomics

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BackgroundHomopolymeric tracts, particularly poly dA.dT, are enriched within the intergenic sequences of eukaryotic genomes where they appear to act as intrinsic regulators of nucleosome positioning. A previous study of the incomplete genome of the human malarial parasite Plasmodium falciparum reports a higher than expected enrichment of poly dA.dT tracts, far above that anticipated even in this highly AT rich genome. Here we report an analysis of the relative frequency, length and spatial arrangement of homopolymer tracts for the complete P. falciparum genome, extending this analysis to twelve additional genomes of Apicomplexan parasites important to human and animal health. In addition, using nucleosome-positioning data available for P. falciparum, we explore the correlation of poly dA.dT tracts with nucleosome-positioning data over key expression landmarks within intergenic regions.ResultsWe describe three apparent lineage-specific patterns of homopolymeric tract organization within the intergenic regions of these Apicomplexan parasites. Moreover, a striking pattern of enrichment of overly long poly dA.dT tracts in the intergenic regions of Plasmodium spp. uniquely extends into protein coding sequences. There is a conserved spatial arrangement of poly dA.dT immediately flanking open reading frames and over predicted core promoter sites. These key landmarks are all relatively depleted in nucleosomes in P. falciparum, as would be expected for poly dA.dT acting as nucleosome exclusion sequences.ConclusionsPrevious comparative studies of homopolymer tract organization emphasize evolutionary diversity; this is the first report of such an analysis within a single phylum. Our data provide insights into the evolution of homopolymeric tracts and the selective pressures at play in their maintenance and expansion.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-848) contains supplementary material, which is available to authorized users.

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“…Previous tool, poly (Bizzaro and Marx, 2003) written in object oriented scripting language Python which gives output having microsatellite locations, tract frequencies and length by command line, thus not user friendly. Pipeline diversity analysis (PDA) (Casillas and Barbadilla, 2004) can search polymorphism in database with genetic diversity estimation without polymorphism and primers for genotyping.…”

Section: Introductionmentioning

confidence: 99%

PolyMorphPredict: A Universal Web-Tool for Rapid Polymorphic Microsatellite Marker Discovery From Whole Genome and Transcriptome Data

et al. 2019

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Microsatellites are ubiquitously distributed, polymorphic repeat sequence valuable for association, selection, population structure and identification. They can be mined by genomic library, probe hybridization and sequencing of selected clones. Such approach has many limitations like biased hybridization and selection of larger repeats. In silico mining of polymorphic markers using data of various genotypes can be rapid and economical. Available tools lack in some or other aspects like: targeted user defined primer generation, polymorphism discovery using multiple sequence, size and number limits of input sequence, no option for primer generation and e-PCR evaluation, transferability, lack of complete automation and user-friendliness. They also lack the provision to evaluate published primers in e-PCR mode to generate additional allelic data using re-sequenced data of various genotypes for judicious utilization of previously generated data. We developed the tool (PolyMorphPredict) using Perl, R, Java and launched at Apache which is available at http://webtom.cabgrid.res.in/polypred/. It mines microsatellite loci and computes primers from genome/transcriptome data of any species. It can perform e-PCR using published primers for polymorphism discovery and across species transferability of microsatellite loci. Present tool has been evaluated using five species of different genome size having 21 genotypes. Though server is equipped with genomic data of three species for test run with gel simulation, but can be used for any species. Further, polymorphism predictability has been validated using in silico and in vitro PCR of four rice genotypes. This tool can accelerate the in silico microsatellite polymorphism discovery in re-sequencing projects of any species of plant and animal for their diversity estimation along with variety/breed identification, population structure, MAS, QTL and gene discovery, traceability, parentage testing, fungal diagnostics and genome finishing.

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Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA

Cited by 23 publications

References 13 publications

ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation

ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation

Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites

PolyMorphPredict: A Universal Web-Tool for Rapid Polymorphic Microsatellite Marker Discovery From Whole Genome and Transcriptome Data

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