FasTAN: A Fast Tandem Repeat Finder

• FasTAN

Overview

FasTAN is a tandem array finder under development. The capabilities of such a utlity can be partitioned into 3 parts: (a) detection of intervals of the subject sequence that contain a tandem array with an estimate of the unit size, (b) partitioning of a detected interval into individual subunits, and (c) reporting a model of the units composing a specific array. The current version of FasTAN can perform (a) and (b) but not yet (c).

FasTAN is part of the "Fast" series of tools developed primarily by EWM. As such its outputs are ONE files describing alignments (files with extension .1aln) or annotations (files with extension .1ano) and a number of useful utilities for manipulating these are in the FASTGA repo which we strongly suggest you also install for this reason. In addition there is a QT-based viewer ALNVIEW that allows you to visualize and peruse the alignments in a .1aln file.

A .1ano file is our version of a BED-file and there are utilites in the FASTGA repo (ANOtoBED and BEDtoANO) that allow you to convert between the two. However, .1ano files can also contain additional information not contemplated by the BED format, such as the partitioning of a TA-interval into units and the display of a model of a unit. For those of you that are not C-programmers and/or do not want to directly work with ONE files, you can convert a binary ONE file into an easy to parse ASCII version with ONEview (which is also in the FASTGA repo).

FasTAN Reference

Usage: FasTAN [-vamp] [-T(8)] [-o<target>] <source:path>[<fa_extn>|<1_extn>|.1gdb]

           <fa_extn> = (.fa|.fna|.fasta)[.gz]
           <1_extn>  = any valid 1-code sequence file type

      -v: Verbose mode, output statistics as proceed.
      -a: Make a .1aln of all the hits found.
      -m: Make a .1ano mask of the hits found.
      -p: Parse hits into units.

      -o: Root path of .1aln/.1ano file (default root path of input).
      -T: Number of threads to use.

FasTAN takes a FASTA, a ONE sequence, or a 1GDB file as input. With the -a option set it produces a .1aln file of the "first-wave" alignments of the tandem arrays it finds. The first wave alignment is that sequence alignment that aligns consequtive units to each other and as such its level of similarity is an indicator of the level of similarity/conservation between the units of the array. With the -m option set it produces a .1ano file of the intervals containining the detected tandem arrays along with an estimate of the average unit size and the average identity of the alignment. If the -p option is set, then the -m option must also be set, and the .1ano file also contains a P-line that describes the partitioning of the TA interval into units.

By default 8 threads are used and the output file names are the root name of the input with a .1aln or .1ano suffix as per the options. You can direct the output to a particular root path with the -o option, and control the number of threads with the -T option.