YASS pipeline

YASS specifications

Information


Unique identifier OMICS_03702
Name YASS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Laurent Noé <>

Information


Unique identifier OMICS_03702
Name YASS
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Laurent Noé <>

Publication for YASS

YASS IN pipelines

 (6)
2017
PMCID: 5485006
PMID: 28261921
DOI: 10.1111/mec.14084

[…] used as a basis for generating locus schemes that were used for following the structural evolution of flc orthologues. gata (nix & eisen 2005), mvista (mayor et al. 2000; frazer et al. 2004), yass (noe & kucherov 2005) and clustalw (larkin et al. 2007; goujon et al. 2010; mcwilliam et al. 2013) were used for different aspects of sequence analysis (details in supplementary methods, […]

2016
PMCID: 5203791
PMID: 27797956
DOI: 10.1093/gbe/evw257

[…] all the assembled contigs using the conserved 5s sequence as a nucleotide query using blastn. second, we use the presence of the flanking genes to further evaluate the contigs. third, we used yass (noé and kucherov 2005) and clustalw (http://www.ch.embnet.org/software/clustalw.html) to identify structural similarities among the contigs., we used a 45s rdna unit with 45,337 bp nucleotides. […]

2016
PMCID: 5218374
PMID: 27707747
DOI: 10.1093/aob/mcw187

[…] sequences were submitted to genbank under accession numbers kt008109 (‘darmor’ l), kt008110 (‘darmor’ s), kt008111 (‘asparagus kale’) and kt008112 (‘yudal’). subrepeats were analysed using the yass genomic similarity search tool (noe and kucherov, 2005) and tandem repeats finder (benson, 1999). a phylogenetic tree was reconstructed using the seaview program (gouy et al., 2010)., […]

2013
PMCID: 3692318
PMID: 23512008
DOI: 10.1038/hdy.2013.11

[…] the genbank database. the rrna coding sequences were identified by pairwise comparisons using dot plot graphical outputs (http://www.vivo.colostate.edu/molkit/dnadot/ and http://bioinfo.lifl.fr/yass/) (noe and kucherov, 2005). sliding windows were set to 9 with stringencies corresponding to 0–1 mismatches. annotation of regulatory motifs was carried out based on analogy with a. thaliana […]

2011
PMCID: 3025954
PMID: 21223577
DOI: 10.1186/1471-2164-12-19

[…] high conservation of dif/xercd systems and the possible loss of dif sequences in endosymbionts, with suggestions for other cdr mechanisms [46]. here, the prediction was based on blast searches and yass alignment [47] with the dif sequences of e. coli and b. subtilis, and candidates were selected based on their proximity to the gc skew shift-points and a single occurrence per chromosome. […]

YASS institution(s)
LORIA/INRIA-Lorraine, Villers-les-Nancy, France

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