YASS(1)

NAME
yass - pairwise aligments of low conserved genomic regions

SYNOPSIS
yass [OPTIONS] {file1.mfas file2.mfas}

DESCRIPTION

yass is a genomic (DNA/RNA) sequence local alignment tool based on subset seeds to reach high sensitivity on low similarity regions. The input format is fasta or multifasta. The output format may be chosen directly and/or modified to match full blast output, axt or fasta format alignments, using the yass2blast.pl script (<http://bioinfo.lifl.fr/yass/files/yass2blast.pl>)

yass accepts any single/multiple seeds as a parameter using the "-p ##-@-#,##--#@#" parameter. Seeds can be designed by hand or by using the hedera tool (<http://bioinfo.lifl.fr/yass/hedera.php>) in order to detect your alignments more efficiently.

OPTIONS

-d <int>, --display <int>
    0.  display positions, length, and E-value (kept for compatibility issues)
    1.  display positions, length, and E-value + statistics and alignments shown (default)
    2.  display a blast tabular output
    3.  display a light tabular output (easier to parse)
    4.  display a BED output (see the BED format specification at <http://genome.ucsc.edu/FAQ/FAQformat#format1>)
    5.  display a PSL output (see the PSL format specification at <http://genome.ucsc.edu/FAQ/FAQformat#format2>)

-r <int>, --reverse <int>
    0.  process forward (first file) strain
    1.  process reverse complement (first file) strain
    2.  process both (default)

-o <str>, --output <str>
    set an output file

-l, --lowercase
    mask lowercase regions : this only takes effect on the index algorithm. It is thus still possible to have lowercase regions in extended parts of an uppercase region, or between two uppercase regions.

-s <int>, --sort <int>
    sort results according to :
    0.  alignment scores
    1.  entropy (interesting on RNA sequences)
    2.  mutual information content (experimental)
    3.  both entropy and scores
    4.  first sequence positions
    5.  second sequence positions
    10-15.
        equivalent to (0-5) + sort by first fasta chunks first
    20-25.
        equivalent to (0-5) + sort by second fasta chunks first
    30-35.
        equivalent to (0-5) + sort by both first/second chunks first
    40-45.
        equivalent to (10-15) + sort chunk results with (0-5) criterion (first fasta file)
    50-55.
        equivalent to (20-25) + sort chunk results with (0-5) criterion (second fasta file)
    60-65.
        equivalent to (30-35) + sort chunk results with (0-5) criterion (first fasta file)
    70-75.
        (30-35) + sort chunk results with (0-5) criterion (second fasta file)
    80-85.
        (30-35) + sort chunk results with (0-5) criterion (both fasta files) (default 70)

-v, --version
    display the current version

-M <int>, --Matrix <int>
    select a predefined scoring matrix :

    [Match,Transversion,Transition],(Gopen,Gext)
    0.  [1,-3,-2],( -8,-2)
    1.  [3,-2,-1],(-12,-4)
    2.  [3,-4,-2],(-16,-4)
    3.  [5,-4,-2],(-16,-4)

-C <int>[,<int>[,<int>[,<int>]]], --Costs <int>[,<int>[,<int>[,<int>]]]
    reset substitution costs for :
    -   match,mismatch
    -   match,mismatch,transition
    -   match,mismatch,transition,other you can also give the 16 values of matrix in the ACGT order.

-G <int>,<int>, --Gaps <int>,<int>
    reset Gap opening/extension penalties

-L <real>,<real>, --Lambda <real>,<real>
    reset Lambda and K parameters of Gumbel law (by default computed)

-X <int>, --Xdrop <int>
    reset Xdrop threshold score (default 25)

-E <float>, --Evalue <float>
    reset E-value threshold (default 10)

-O <int>, --nbO <int>
    limit number of alignments in the output (default 5000000)

-S <int>, --nbS <int>
    select the chunk sequence from the first multi-fasta sequence (default 1 is the first one). Note that the -S 0 parameter enumerates all the chunks of the first multifasta sequence

-T <int>, --Tandems <int>
    forbid aligning too close regions (e.g. Tandem repeats) valid for single sequence comparison only (default 16 bp)

-c <int>, --hitcriterion <int>
    select the hit criterion, i.e. number of single hit needed to consider a match, it can be 1 (single hit criterion) as blast or 2 (default behavior).

-p <str>[,str...], --pattern <str>[,str...]
    seed pattern, represented over the alphabet {'#','@','-'}. Each seed is a string and you are allowed to use several seed patterns separated by ','
    -   symbol '#' is a must-match position, pair of nucleotides under these positions must have to be similar.
    -   symbol '@' is a transition-free position, pair of nucleotides under these positions have to be in the same purin-purin or pyrimidin-pyrimidin group. Thus transitions mismatches are allowed by this element.
    -   symbol '-' is called joker, in the sense that any pair of nucleotides is allowed.

    you are allowed to use at most 32 seeds

    examples :
    -
          yass file.fas -p "#@#--##--#-##@#"
    -
          yass file.fas -p "##-#-#@#-##@-##,##@#--@--##-#--###"

-e <real>, --entropy <real>
    minimal allowed Entropy of trinucleotide distribution. Range between 0 (no filter) and 6, default 2.80

-t <real>, --trim <real>
    trim out over-represented seeds codes, range between 0.0 (no trim) and +inf, default 0.001

-a <int>, --alpha <int>,
    statistical tolerance Alpha (%), (default 5%) : it gives the percent of allowed runs of seeds that may be missed on a waiting time distribution, and thus separated into two alignments.

-i <int>, --indels <int>,
    Indel rate (%) used in the waiting time distribution

-m <int>, --mutations <int>
    Mutation rate (%) used in the waiting time distribution

-W <int>,<int>, --Windows <int>
    In order to group some consecutive alignments into a better scoring one, post processing tries to group neighbor alignments in an iterative process : by applying several time a sliding windows on the text and estimating score of possible groups formed. Windows size can be controlled according to a geometric pattern -w <mul> and two bounds -W <min,max>.

-w <real>, --window <real>
    Window geometric pattern (see -W option)

NOTES

yass post processing can be disabled with the "-w 0" parameter. Repeats filters can be almost disabled with some " -e 0 -t 0 -E 1000000 -O 1000000 " parameter.

The last of any -C , -G options and -M option overrides the previous ones.

yass main page is <http://bioinfo.lifl.fr/yass/>, a web-server is available at <http://bioinfo.lifl.fr/yass/yass.php>

SEE ALSO
blast2(1),wise(1),sim4(1)