# tantan

# Introduction

tantan is a tool for masking simple regions (low complexity and short-period tandem repeats) in biological sequences.

The aim of tantan is to prevent false predictions when searching for homologous regions between two sequences. Simple repeats often align strongly to each other, causing false homology predictions.

# Setup

You need to have a C++ compiler. On Linux, you might need to install a package called "g++". On Mac, you might need to install command-line developer tools. On Windows, you might need to install Cygwin.

Using the command line, go into the tantan directory. To compile it, type:

    make

Optionally, copy tantan to a standard "bin" directory (using "sudo" to request administrator permissions):

    sudo make install

Or copy it to your personal bin directory:

    make install prefix=~

You might need to log out and back in for your computer to recognize the new program.

# Normal usage

- Suppose you have some nucleotide sequences (DNA or RNA) in a FASTA-format file called "ntseqs.fa". You can identify simple repeats like this:

      tantan ntseqs.fa > masked.fa

  This will create a new FASTA file called "masked.fa" that replaces all masked regions with lowercase letters. (tantan also works on FASTQ-format, though it does not use the quality data.)

- To mask proteins effectively, tantan needs to use different algorithm parameters than for nucleotides. You have to tell it when you have proteins, using the "-p" option:

      tantan -p aaseqs.fa > masked.fa

  If you omit "-p" and the sequences look proteinaceous, tantan will print a warning message.

# Advanced usage

- By default, tantan indicates repetitive regions with lowercase letters. You can make it replace repetitive letters with (say) "N" by using the "-x" option:

      tantan -x N ntseqs.fa > masked.fa

- By default, tantan does not preserve lowercase letters in the input sequences. You can tell it to preserve them by using the "-c" option. So the output will have the union of the lowercase in the input and the lowercase assigned by tantan:

      tantan -c ntseqs.fa > masked.fa

- tantan's masking rate is usually OK, but you can alter it by changing the "-r" parameter from its default value of 0.005. Higher values increase the amount of masking, and lower values decrease it. This increases the masking rate:

      tantan -r 0.02 ntseqs.fa > masked.fa

- Finally, to mask extremely AT-rich DNA, you should change tantan's scoring matrix. The "test" directory contains a matrix "atMask.mat" that works well for DNA with ~80% A+T, such as Plasmodium and Dictyostelium genomes. We recommend masking such DNA like this:

      tantan -m atMask.mat -r 0.01 atrich.fa > masked.fa

The preceding examples cover all of tantan's options that you should ever need.

# Recommendations for homology search

1. Mask both (sets of) sequences.
2. If for some reason you wish to mask only one (set of) sequence(s), increase "-r" to 0.02 (0.05 for AT-rich DNA).
3. For DNA-versus-protein alignment, increase "-r" for the proteins to 0.02. If for some reason you mask only one (set of) sequence(s), make sure it's the proteins.
4. Some alignment tools exclude lowercase from their initial seeding phase, but treat lowercase identically to uppercase during their subsequent extension phase. Unfortunately, this does not reliably prevent false homology predictions. It is OK to re-align without masking after homology has been decided: FASTA and LAST can do this.

For more information, please read the tantan publication (see below).

# FAQ

## Why does tantan sometimes mask isolated bases?

This happens when a region is borderline repetitive, and a single base creeps just over the threshold. Don't worry about it, it's not a problem (at least for tantan's aim of preventing false homology).

## Does tantan mask functional sequence?

Of course. Proteins and protein-coding exons can contain simple repeats. Repeats can be functional. If we want to avoid false homology we have to mask them. Remember that tantan merely lowercases repeats, so it's easy to lift the masking after determining homology.

# Options

`-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 score matrix
`-r` | probability of a repeat starting per position
`-e` | probability of a repeat ending per position
`-w` | maximum tandem repeat period to consider
`-d` | probability decay per period (period-(i+1) / period-i)
`-i` | match score
`-j` | mismatch cost
`-a` | gap existence cost
`-b` | gap extension cost
`-s` | minimum repeat probability for masking
`-n` | minimum copy number, affects -f4 only
`-f` | output type: 0=masked sequence, 1=repeat probabilities, 2=repeat counts, 3=BED, 4=tandem repeats
`-h, --help` | show help message, then exit
`--version` | show version information, then exit

# Advanced issues

When tantan masks tandem repeats, it tends to leave the first (left-most) repeat unit unmasked. This sometimes allows us to find homologs we would otherwise miss:

    TGCAAGCTA TTAGGCTTAGGTCAGTGC ttaagcttaggtcagtgc AACATA
    ||| ||| | |||||||||||||||||| ||| |||||||||||||| ||| ||
    TGCTAGCAA TTAGGCTTAGGTCAGTGC ttaggcttaggtcagtgc AACGTA

However, there is a danger of non-equivalent repeat units being unmasked. This happens especially if we mask DNA on one strand but align it on the other strand:

                       TGCAAGCTA TTAGGCTTAGGTCAGTGC ttaagcttaggtcagtgc AACATA
                                 ||||||||||||||||||
    TGCTAGCAA ttaggcttaggtcagtgc TTAGGCTTAGGTCAGTGC AACGTA

(My thanks to Junko Tsuji and Paul Horton for finding these issues.)

# Finding straightforward tandem repeats

Option -f4 runs tantan in a different mode, where it finds straightforward tandem repeats only. (Technically, it uses a Viterbi algorithm instead of a Forward-Backward algorithm.) This is not recommended for avoiding false homologs! But it might be useful for studying tandem repeats. The output looks like this:

    mySeq   14765   14780   6       2.5     GTCATG  GTCATG,GTCATG,GTC
    mySeq   632362  632377  2       6       GC      GC,GC,GC,GCt,GCT,GCT
    mySeq   1278353 1278369 3       6.5     TCA     TCA,TCA,TCA,TC-,TC,TC,T
    mySeq   3616084 3616100 3       5.33333 TGG     TGA,TGA,TGG,TGG,TGG,T

The first 3 columns show the start and end coordinates of the repetitive region, in BED format. Column 4 shows the length of the repeating unit (which might vary due to insertions and deletions, so this column shows the most common length). Column 5 shows the number of repeat units. Column 6 shows the repeating unit (which again might vary, so this is just a representative). Column 7 shows the whole repeat: lowercase letters are insertions relative to the previous repeat unit, and dashes are deletions relative to the previous repeat unit.

# Miscellaneous

tantan is distributed under the GNU General Public License, either version 3 of the License, or (at your option) any later version. For details, see COPYING.txt.

If you use tantan in your research, please cite: "A new repeat-masking method enables specific detection of homologous sequences", MC Frith, Nucleic Acids Research 2011 39(4):e23.

tantan's website is: http://www.cbrc.jp/tantan/

If you have any questions, comments, or problems concerning tantan, please email: tantan (ATmark) cbrc (dot) jp.