yass

(more at http://bioinfo.univ-lille.fr/yass/)

yass is a genomic similarity seach tool for nucleic (and only nucleic) sequences in (multi)fasta or plain text format. yass produces local pairwise alignments in yass format, blast tabular format, or PSL format.

The associated tool yass2blast.pl may be used to convert the default yass output into blast full output, into fasta alignments, or into AXT format.

The associated tool yass2dotplot.php could also be used to convert the default yass output into png or svg dotplots.

Installation

(more at http://bioinfo.univ-lille.fr/yass/download.php)

You need a C compiler and the autotools. On Linux, you can install gcc, autoconf, automake. On Mac, you can install xcode, or the command line developer tools (or you can use macports to install gcc for example).

Using the command line, type:

git clone https://github.com/laurentnoe/yass.git
cd yass
./configure --with-threads
make

or:

git clone https://github.com/laurentnoe/yass.git
cd yass
autoreconf
./configure --with-threads
automake
make

you can install yass to a standard /local/bin directory:

sudo make install

or copy the binary directly to your homedir:

cp src/yass ~/.

Command-line

(more at http://bioinfo.univ-lille.fr/yass/help.php)

common usage

-d <N>	where N = [0..5], to select the output format (default is 1)
-r <N>	where N = [0..2] to select the forward, reverse, or both sense on the first sequence (default is both)
-S <N>	to select only one sequence in the first multifasta file (give a number between 1 and nbparts). By default all the sequences are processed.

scoring system

-C <N,...>	with 2,3,4 or 16 parameters to give the: Match/Mismatch scores, Match/Transition/Transversion scores, Match/Transition/Transversion/Other IUPAC scores, 4x4 ACGT matrix (and disable scoring correction algorithm).
-G <No,Ne>	with two parameters to change the cost for: the very first gap opening No, the subsequent extension costs Ne.
-E <N>	to set the E-value threshold N (default 10).
-X <N>	to set the X-drop threshold score N (default 25).

and

-L <Nl,Nk>

to possibly change the Lambda Nl and K Nk values if the one computed do not correspond to your needs. (Note that the ALP tool can do the work: https://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/software/program.html?uid=6 )

search parameters

-p <"seedpattern">
	where the seed pattern is one, or several seeds separated by comma, where each seed is a word on the "#@-" alphabet (Note that the Iedera tool can do the design: https://github.com/laurentnoe/iedera or http://bioinfo.univ-lille.fr/yass/iedera.php ) another possibility is to use "Minimally overlapping words" such as the pattern "RYNNNNNnnnNNNN" to speed-up the search, but at a lower sensitivity.
-c <N>	where N = [1..2] for single or double hit criterion

Example

A very small example:

yass                   file1.fa  file2.mfa >  yass-output.yop
yass2blast.pl  -blast  yass-output.yop     >  blastlike-output.blk
yass2dotplot.php       yass-output.yop  filename1=""  filename2="" ; open dp.png

A second example where the scoring system is modified, the E-value changed:

yass    file1.fa  file2.mfa    -C 2,-2,-3   -G -5,-2   -E 1e-3   -o yass-output.yop

References

how to cite this tool:

Noe L., Kucherov G., YASS: enhancing the sensitivity of DNA similarity search, 2005, Nucleic Acids Research, 33(2):W540-W543. <http://doi.org/10.1093/nar/gki478>