TRF pipeline

TRF specifications

Information


Unique identifier OMICS_03537
Name TRF
Alternative name Tandem Repeats Finder
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data DNA sequence
Input format FASTA
Operating system Unix/Linux
Computer skills Medium
Version 4.09
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Yozen Herndez <>
  • person_outline Gary Benson <>

Information


Unique identifier OMICS_03537
Name TRF
Alternative name Tandem Repeats Finder
Interface Web user interface
Restrictions to use None
Input data DNA sequence
Input format FASTA
Computer skills Basic
Version 4.09
Stability Stable
Maintained Yes

Maintainers


  • person_outline Yozen Herndez <>
  • person_outline Gary Benson <>

Publication for Tandem Repeats Finder

TRF citations

 (17)
2018
PMCID: 5833319

[…] start of trnaval, whereas the 5ʹ end was determined by comparing orthologous sequences of other known mitogenomes. the entire a+t-rich region was subjected to a search for the tandem repeats using tandem repeats finder program (benson 1999). composition skew was used to describe the base composition of nucleotide sequences, with the relative number of as to ts (at skew = [a – t]/[a + t]) […]

2018
PMCID: 5893962

[…] by blastn on the ncbi website and then validated by performing a homologous gene alignment against other plant bugs. furthermore, the entire control region was examined for tandem repeats using the tandem repeats finder program (benson 1999)., phylogenetic analyses were performed based on 14 complete representative bug mt genomes from genbank, and 11 miridae species as follows: lygus hesperus […]

2018
PMCID: 5943242

[…] 45snrdna sequences from 28 brassica and raphanus genotypes (tables s2–s5). putative snps and indels were manually analyzed using the file aligned with mega7. tandem repeats were identified using the tandem repeats finder (trf) tool. to detect highly reliable variations, all predicted variations were manually curated for both chloroplast and 45snrdna. some of the randomly selected and highly […]

2017
PMCID: 5435911

[…] and a file that contained the first read that was not merged by flash was used for further analysis for each of the replicates (18). next, we identified repetitive sequences within reads by applying tandem repeats finder (trf) software to all files (19). the trf output file was converted from dat file format to fastq format., alignment to the mouse mitochondrial genome was performed using […]

2015
PMCID: 4332147

[…] visualized with geneious 6.1 software (biomatters ltd., auckland, new zealand; http://www.geneious.com/) to ensure quality sequences and were examined for microsatellite regions using the online tandem repeats finder (benson, 1999). primers were designed using the program primer3 (rozen and skaletsky, 1999) for 24 sequenced fragments containing appropriate microsatellite regions […]

TRF institution(s)
Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, NY, USA
TRF funding source(s)
This work was partially supported by NSF grant CCR-9623532.

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