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Protocols

TRDB specifications

Information


Unique identifier OMICS_03538
Name TRDB
Alternative name Tandem Repeats DataBase
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Version 2.30
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Tandem_Repeats_Database

Subtool


  • TRF (Tandem Repeats Finder)

Publication for Tandem Repeats DataBase

TRDB citations

 (7)
library_books

Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome

2016
PLoS Genet
PMCID: 5035033
PMID: 27662467
DOI: 10.1371/journal.pgen.1006317

[…] d for mapping neocentromere coordinates. Inverted repeats were identified with the Inverted Repeats Database (https://tandem.bu.edu/cgi-bin/irdb/irdb.exe), and tandem repeats were identified with the Tandem Repeats Database (https://tandem.bu.edu/cgi-bin/trdb/trdb.exe). GC% and GC skew ((G-C)/(G+C)) was calculated with FastPCR. Gene essentiality information for homologs of C. albicans genes was ob […]

library_books

Identification and characterization of a minisatellite contained within a novel miniature inverted repeat transposable element (MITE) of Porphyromonas gingivalis

2015
Mob DNA
PMCID: 4596501
PMID: 26448788
DOI: 10.1186/s13100-015-0049-1

[…] Both DNA strands, as well as intergenic and coding sequences, were queried separately. Mismatches of ‘0’ through ‘3’ were allowed, with the constraint of the ‘mismatch type’ being a substitution.The Tandem Repeats Database software was used for determining all types of tandem repeat elements in the P. gingivalis genomes (strains ATCC 33277 and W83 hosted on the server as of 12/2013), and to deter […]

call_split

Genome wide analysis of tandem repeats in Tribolium castaneum genome reveals abundant and highly dynamic tandem repeat families with satellite DNA features in euchromatic chromosomal arms

2015
PMCID: 4675708
PMID: 26428853
DOI: 10.1093/dnares/dsv021
call_split See protocol

[…] mat from the web page ftp://ftp.bioinformatics.ksu.edu/pub/BeetleBase/3.0/ (The third version of the assembly: Tcas_3.0) in the form of 10 chromosomes. The sequence of each chromosome was uploaded to Tandem Repeats Database (TRDB), https://tandem.bu.edu/cgibin/trdb/trdb.exe and analysed using Tandem Repeats Finder (TRF) algorithm. All chromosomes have been processed with TRF using alignment parame […]

library_books

GTAG and CGTC tagged palindromic DNA repeats in prokaryotes

2013
BMC Genomics
PMCID: 3733652
PMID: 23902135
DOI: 10.1186/1471-2164-14-522

[…] uring 7–8 base paired residues, separated by loops of variable lengths. Some repeats were identified by searching abundant, self-complementary sequences in individual prokaryotic genomes by using the TRDB (Tandem Repeats Database) facility [].The organization of the various repeat families was assessed by using the Fuzznuc program of the EMBOSS package. Genomes of interest were searched for SLSs h […]

library_books

Transposable Elements Are a Significant Contributor to Tandem Repeats in the Human Genome

2012
Comp Funct Genomics
PMCID: 3389668
PMID: 22792041
DOI: 10.1155/2012/947089

[…] Output from TRDB for all TRs in the human genome was filtered using an in-house Perl script such that they meet the following criteria: repeat unit length ≥20 bp, GC content ≥40%, repeat number ≥2, and sequence s […]

library_books

Gene Discovery in the Threatened Elkhorn Coral: 454 Sequencing of the Acropora palmata Transcriptome

2011
PLoS One
PMCID: 3247206
PMID: 22216101
DOI: 10.1371/journal.pone.0028634

[…] ried out using wego (http://wego.genomics.org.cn/cgi-bin/wego/index.pl) .To detect repeat elements, the full set of sequences was uploaded to the Tandem Repeats Database (http://tandem.bu.edu/cgi-bin/trdb/trdb.exe) and searched using tandem repeats finder v4.04 . Repeats between 2 and 6 bp were considered and comparisons were made with microsatellite frequencies from the publicly available A. mil […]

Citations

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TRDB institution(s)
Lab for Biocomputing and Informatics, Boston University, Boston, MA, USA; Department of Computer Science, Boston University, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA; Department of Neuroscience, Mount Sinai School of Medicine, New York, NY, USA
TRDB funding source(s)
Partially supported by National Science Foundation grants DBI-0090789, CCR-0073081, DBI-0413462 and IIS-0612153.

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