This is the command tantan that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
tantan - low complexity and tandem repeat masker for biosequences
SYNOPSIS
tantan [options] fasta-sequence-file(s)
DESCRIPTION
Find simple repeats in sequences
Options (default settings):
-p interpret the sequences as proteins
-x letter to use for masking, instead of lowercase
-c preserve uppercase/lowercase in non-masked regions
-m file for letter pair scores (+1/-1, but -p selects BLOSUM62)
-r probability of a repeat starting per position (0.005)
-e probability of a repeat ending per position (0.05)
-w maximum tandem repeat period to consider (100, but -p selects 50)
-d probability decay per period (0.9)
-a gap existence cost (0)
-b gap extension cost (infinite: no gaps)
-s minimum repeat probability for masking (0.5)
-f output type: 0=masked sequence, 1=repeat probabilities,
2=repeat counts, 3=BED (0)
-h, --help
show help message, then exit
--version
show version information, then exit
REPORTING BUGS
Report bugs to: [email protected]
Home page: http://www.cbrc.jp/tantan/
Use tantan online using onworks.net services
