TRF

NAME

trf - locate and display tandem repeats in DNA sequences

SYNOPSIS

trf (File|Match|Mismatch|Delta|PM|PI|Minscore|MaxPeriod) [options]

OPTIONS

Where: (all weights, penalties, and scores are positive)

	File		sequences input file
	Match		matching weight

Mismatch

mismatching penalty

	Delta		indel penalty
	PM		match probability (whole number)
	PI		indel probability (whole number)

Minscore

minimum alignment score to report

MaxPeriod

maximum period size to report

[options] = one or more of the following:

	-m		masked sequence file
	-f		flanking sequence
	-d		data file
	-h		suppress html output
	-r		no redundancy elimination

-l <n>

maximum TR length expected (in millions) (eg, -l 3 or -l=3 for 3 million) Human genome HG38 would need -l 6

-ngs

more compact .dat output on multisequence files, returns 0 on success. Output is printed to the screen, not a file. You may pipe input in with this option using - for file name. Short 50 flanks are appended to .dat output.

SEE ALSO

See more information on the TRF Unix Help web page: https://tandem.bu.edu/trf/trf.unix.help.html

NOTE

Note the sequence file should be in FASTA format:

>Name of sequence aggaaacctgccatggcctcctggtgagctgtcctcatccactgctcgctgcctctccag atactctgacccatggatcccctgggtgcagccaagccacaatggccatggcgccgctgt actcccacccgccccaccctcctgatcctgctatggacatggcctttccacatccctgtg

AUTHOR

Copyright © 1999-2020 Gary Benson

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.