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TRDB--The Tandem Repeats Database

Gelfand, Y., Rodriguez, A., Benson, G.·2007·Nucleic Acids Research
DOI 10.1093/nar/gkl1013PMC PMC1781109
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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

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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

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