(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.
(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 ~/.
(more at http://bioinfo.univ-lille.fr/yass/help.php)
| -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. |
| -C <N,...> | with 2,3,4 or 16 parameters to give the:
|
| -G <No,Ne> | with two parameters to change the cost for:
|
| -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 ) |
| -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 |
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
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>