CoChat
Sign Up
Cited by 159

The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.

TRDB--The Tandem Repeats Database

Gelfand, Y., Rodriguez, A., Benson, G.·2007·Nucleic Acids Research
DOI 10.1093/nar/gkl1013PMC PMC1781109
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/nar/gkl1013

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Figures

Figure 1 Repeat tables for the human genome (hg18 obtained from the UCSC genome browser website). Upper panel: TRF computed characteristics for repeats from chromosome 1. Filters applied were pattern size ≥ 25, copy number ≥ 5.0. Note that the third and fourth repeats redundantly report the same locus because of TRF reporting criteria (the larger pattern gives at least a 10% better alignment score). Note also that repeats with pattern sizes 25 and 26 are essentially AT repeats with some slight variations. This can be inferred from the percentage nucleotide columns and quickly checked by clicking on the repeat indices which opens an alignment window (see Figure 2 for an example). Middle panel: TRDB computed characteristics for repeats drawn from the entire genome. The repeats in this table have the potential to cause frame shift mutations. They have periods of 4 or 5 (rather than a multiple of 3), are contained exclusively in exons, and have a high percent matching which is typical of microsatellites that undergo replication slippage. The 4 unchecked repeats contain at least 14 exact copies in a row (as determined by visual inspection of their alignments). Lower panel: The filter used to obtain the middle table.
Figure 1 Repeat tables for the human genome (hg18 obtained from the UCSC genome browser website). Upper panel: TRF computed characteristics for repeats from chromosome 1. Filters applied were pattern size ≥ 25, copy number ≥ 5.0. Note that the third and fourth repeats redundantly report the same locus because of TRF reporting criteria (the larger pattern gives at least a 10% better alignment score). Note also that repeats with pattern sizes 25 and 26 are essentially AT repeats with some slight variations. This can be inferred from the percentage nucleotide columns and quickly checked by clicking on the repeat indices which opens an alignment window (see Figure 2 for an example). Middle panel: TRDB computed characteristics for repeats drawn from the entire genome. The repeats in this table have the potential to cause frame shift mutations. They have periods of 4 or 5 (rather than a multiple of 3), are contained exclusively in exons, and have a high percent matching which is typical of microsatellites that undergo replication slippage. The 4 unchecked repeats contain at least 14 exact copies in a row (as determined by visual inspection of their alignments). Lower panel: The filter used to obtain the middle table.CC BY-NC · PubMed Central
Figure 2 View of a tandem array aligned with its consensus pattern. This repeat is from human chromosome 5 (hg18, indices 720 890–721 608). The pattern size is 48 and the array contains 14.9 copies. The top line is the consensus. Dashes in the top line indicate an insertion relative to the consensus in one or more of the copies. Remaining bars represent consecutive copies in the tandem array. Only substitutions, insertions and deletions relative to the consensus are displayed as separate characters. When the repeat has a fractional copy, the final bar shows the point where the repeat terminates. This repeat is predicted to be polymorphic. Note that there are eight columns where repetitive point mutations occur and at least three groupings of these mutations suggest that the repeat has undergone multiple rounds of expansion. These are the A,T,G,G grouping that appears four times (one of which is in copy 4), the related A,T grouping that appears three times (one in copy 3) and the T,C,A grouping that appears twice (one in copy 1).
Figure 2 View of a tandem array aligned with its consensus pattern. This repeat is from human chromosome 5 (hg18, indices 720 890–721 608). The pattern size is 48 and the array contains 14.9 copies. The top line is the consensus. Dashes in the top line indicate an insertion relative to the consensus in one or more of the copies. Remaining bars represent consecutive copies in the tandem array. Only substitutions, insertions and deletions relative to the consensus are displayed as separate characters. When the repeat has a fractional copy, the final bar shows the point where the repeat terminates. This repeat is predicted to be polymorphic. Note that there are eight columns where repetitive point mutations occur and at least three groupings of these mutations suggest that the repeat has undergone multiple rounds of expansion. These are the A,T,G,G grouping that appears four times (one of which is in copy 4), the related A,T grouping that appears three times (one in copy 3) and the T,C,A grouping that appears twice (one in copy 1).CC BY-NC · PubMed Central
Figure 3 View of four related repeats found by the clustering tool, shown as a multiple alignment, from a cluster containing 19 repeats discovered in human chromosome 1 (hg18). These repeats exhibit minor variations, including differences in copy number and are widely spaced along the chromosome (1: 25, 032, 377–25, 032, 662; 2: 63, 711, 700–63, 711, 975; 3: 112, 638, 002–112, 638, 328; 4: 147, 399, 764–147, 400, 090). Note that repeat 1 is present in a reverse complement orientation (RC notation). The top repeat is considered the “master” and all alignments are to its consensus (top line). The master may be picked manually, or TRDB will choose it as the repeat with the smallest combined alignment distance to the remaining repeats. For every other repeat, a consensus bar is shown and the initial and final repeat bars show where the repeat starts and ends relative to the master consensus. Note that repeat 1 starts at a different position than the other three.
Figure 3 View of four related repeats found by the clustering tool, shown as a multiple alignment, from a cluster containing 19 repeats discovered in human chromosome 1 (hg18). These repeats exhibit minor variations, including differences in copy number and are widely spaced along the chromosome (1: 25, 032, 377–25, 032, 662; 2: 63, 711, 700–63, 711, 975; 3: 112, 638, 002–112, 638, 328; 4: 147, 399, 764–147, 400, 090). Note that repeat 1 is present in a reverse complement orientation (RC notation). The top repeat is considered the “master” and all alignments are to its consensus (top line). The master may be picked manually, or TRDB will choose it as the repeat with the smallest combined alignment distance to the remaining repeats. For every other repeat, a consensus bar is shown and the initial and final repeat bars show where the repeat starts and ends relative to the master consensus. Note that repeat 1 starts at a different position than the other three.CC BY-NC · PubMed Central
Figure 4 Histograms illustrating distinctly different distributions of tandem repeat pattern sizes in C.elegans (upper panel) and human (lower panel). Note the significant overrepresentation in humans of microsatellite repeats with periods 1, 2 and 4.
Figure 4 Histograms illustrating distinctly different distributions of tandem repeat pattern sizes in C.elegans (upper panel) and human (lower panel). Note the significant overrepresentation in humans of microsatellite repeats with periods 1, 2 and 4.CC BY-NC · PubMed Central
Figure 5 A view from the browser. Here a single tandem repeat (hg 18, chromosome 1: 21, 678, 941–21, 682, 295), boxed, covers both introns and exons of a gene. The repeat has 2.2 copies of a pattern of 1583 nt. The periodic nature of the introns and exons can be clearly seen. This repeat clusters with six others on chromosome 1, some of which do not overlap any genes.
Figure 5 A view from the browser. Here a single tandem repeat (hg 18, chromosome 1: 21, 678, 941–21, 682, 295), boxed, covers both introns and exons of a gene. The repeat has 2.2 copies of a pattern of 1583 nt. The periodic nature of the introns and exons can be clearly seen. This repeat clusters with six others on chromosome 1, some of which do not overlap any genes.CC BY-NC · PubMed Central

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 4 references

Research works printed but not linked: 30

  1. [1]Kit S. Equilibrium sedimentation in density gradients of DNA preparations from animal tissues J. Mol. Biol. 1961 3 711 716 14456492
  2. [2]La Spada A.R. Wilson E.M. Lubahn D.B. Harding A.E. Fischbeck K.H. Androgen receptor gene mutations in X-linked spinal and bulbar muscular atrophy Nature 1991 352 77 79 2062380
  3. [5]Campuzano V. Montermini L. Molto M.D. Pianese L. Cossee M. Cavalcanti F. Monros E. Rodius F. Duclos F. Monticelli A. Friedreich's ataxia: Autosomal recessive disease caused by an intronic GAA triplet repeat expansion Science 1996 271 1423 1427 8596916
  4. [6]Fu Y.-H. Pizzuti A. Fenwick R.G. Jr King J. Rajnarayan S. Dunne P.W. Dubel J. Nasser G.A. Ashizawa T. DeJong P. An unstable triplet repeat in a gene related to myotonic muscular dystrophy Science 1992 255 1256 1258 1546326
  5. [7]Koob M.D. Moseley M.L. Schut L.J. Benzow K.A. Bird T.D. Day J.W. Ranum L.P. An untranslated CTG expansion causes a novel form of spinocerebellar ataxia (SCA8) Nature Genet. 1999 21 379 384 10192387
  6. [8]Holmes S.E. O'Hearn E.E. McInnis M.G. Gorelick-Feldman D.A. Kleiderlein J.J. Callahan C. Kwak N.G. Ingersoll-Ashworth R.G. Sherr M. Sumner A.J. Expansion of a novel CAG trinucleotide repeat in the 5′ region of PPP2R2B is associated with SCA12 Nature Genet. 1999 23 391 392 10581021
  7. [9]Vandenbergh D. Persico A.M. Uhl G.R. A human dopamine transporter cDNA predicts reduced glycosylation, displays a novel repetitive element and provides racially-dimorphic TaqI RFLPs Mol. Brain Res. 1992 15 161 166 1359373
  8. [10]Cook E.H. Jr Stein M.A. Krasowski M.D. Cox N.J. Olkon D.M. Kieffer J.E. Leventhal B.L. Association of attention-deficit disorder and the dopamine transporter gene Am. J. Hum. Genet. 1995 56 993 998 7717410 PMC1801209
  9. [11]Gilbert D.L. Wang Z. Sallee F.R. Ridel K.R. Merhar S. Zhang J. Lipps T.D. White C. Badreldin N. Wassermann E.M. Dopamine transporter genotype influences the physiological response to medication in ADHD Brain 2006 129 2038 2046 16760197
  10. [12]Lott D. Kim S.J. Cook E.H. Jr de Wit H. Dopamine transporter gene associated with diminished subjective response to amphetamine Neuropsychopharmacology 2005 30 602 609 15602501
  11. [13]Guindalini C. Howard M. Haddley K. Laranjeira R. Collier D. Ammar N. Craig I. O'Garag C. Bubb V.J. Greenwood T. A dopamine transporter gene functional variant associated with cocaine abuse in a Brazilian sample Proc. Natl Acad. Sci. USA 2006 103 4552 4557 16537431 PMC1450209
  12. [14]Klenova E. Scott A.C. Roberts J. Shamsuddin S. Lovejoy E.A. Bergmann S. Bubb V.J. Royer H.-D. Quinn J.P. YB-1 and CTCF differentially regulate the 5-HTT polymorphic intron 2 enhancer which predisposes to a variety of neurological disorders J. Neurosci. 2004 24 5966 5973 15229244 PMC6729234
  13. [15]Cook E.H. Jr Courchesne R. Lord C. Cox N.J. Yan S. Lincoln A. Haas R. Courchesne E. Leventhal B.L. Evidence of linkage between the serotonin transporter and autistic disorder Mol. Psychiatry 1997 2 247 250 9152989
  14. [16]Murphy G. Jr Hollander S.B. Rodrigues H.E. Kremer C. Schatzberg A.F. Effects of the serotonin transporter gene promoter polymorphism on mirtazapine and paroxetine efficacy and adverse events in geriatric major depression Arch. Gen. Psychiatry 2004 61 1163 1169 15520364
  15. [17]Owerbach D. Gabbay K.H. Localization of a type 1 diabetes susceptibility locus to the variable tandem repeat region flanking the insulin gene Diabetes 1993 42 1708 1714 8243816
  16. [19]Stam M. Belele C. Dorweiler J.E. Chandler V.L. Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation Genes Dev. 2002 16 1906 1918 12154122 PMC186425
  17. [20]Alleman M. Sidorenko L. McGinnis K. Seshadri V. Dorweiler J.E. White J. Sikkink K. Chandler V.L. An RNA-dependent RNA polymerase is required for paramutation in maize Nature 2006 442 295 298 16855589
  18. [21]Fondon J.W. III Garner H.R. Molecular origins of rapid and continuous morphological evolution Proc. Natl Acad. Sci. USA 2004 101 18058 18063 15596718 PMC539791
  19. [23]Rozen S. Skaletsky H Krawetz S. Misener S. Primer3 on the WWW for general users and for biologist programmers Bioinformatics Methods and Protocols: Methods in Molecular Biology 2000 Humana Press 365 386 10547847
  20. [24]Gribskov M. McLachlan A.D. Eisenberg D. Profile analysis: Detection of distantly related proteins Proc. Natl Acad. Sci. USA 1987 84 4355 4358 3474607 PMC305087
  21. [25]Maes M. On a cyclic string-to-string correction problem Information Processing Letters 1990 35 73 78
  22. [26]Rao S. Rodriguez A. Benson G. Evaluating distance functions for clustering tandem repeats Genome Inform. 2005 16 3 12 16362901
  23. [27]Kaufman L. Rousseeuw P.J. Finding Groups in Data: An Introduction to Cluster Analysis 1990 New York John Wiley and Sons
  24. [28]Denoeud F. Vergnaud G. Benson G. Predicting human minisatellite polymorphism Genome Res. 2003 13 856 867 12695323 PMC430879
  25. [29]Benson G. Dong L. Reconstructing the duplication history of a tandem repeat Seventh International Conference on Intelligent Systems for Molecular Biology—ISMB99 1999 44 53 10786285
  26. [30]Kolpakov R. Bana G. Kucherov G. mreps: efficient and flexible detection of tandem repeats in DNA Nucleic Acids Res. 2003 31 3672 3678 12824391 PMC169196
  27. [31]Delgrange O. Rivals E. STAR: an algorithm to search for tandem approximate repeats Bioinformatics 2004 20 2812 2820 15180940
  28. [32]Naslund K. Saetre P. von Salome J. Bergstrom T.F. Jareborg N. Jazin E. Genome-wide prediction of human VNTRs Genomics 2005 85 24 35 15607419
  29. [33]Wren J. Forgacs E. Fondon J. Pertsemlidis A. Cheng S. Gallardo T. Williams R. Shohet R. Minna J. Garner H. Repeat polymorphisms within gene regions: phenotypic and evolutionary implications Am. J. Hum. Genet. 2000 67 345 56 10889045 PMC1287183
  30. [34]Fondon J.W. III Mele G.M. Brezinschek R.I. Cummings D. Pande A. Wren J. O'Brien K.M. Kupper K.C. Wei M.H. Lerman M. Computerized polymorphic marker identification: experimental validation and a predicted human polymorphism catalog Proc. Natl Acad. Sci. USA 1998 95 7514 7519 9636181 PMC22669

Cited by

Sorted by citations

See all 159

Metadata

Authors
Gelfand, Y., Rodriguez, A., & Benson, G.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2007-01-03
Volume
35
Issue
Database
Pages
D80-D87
ISSN
  • 0305-1048
  • 1362-4962
DOI
10.1093/nar/gkl1013
PMC
PMC1781109
Cited by
159
References
4
Language
en

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: TRDB--The Tandem Repeats Database. https://app.cochat.ai/papers/10.1093/nar/gkl1013
The paper
Gelfand, Y., Rodriguez, A., & Benson, G. (2007). TRDB--The Tandem Repeats Database. Nucleic Acids Research. https://doi.org/10.1093/nar/gkl1013