YASS protocols

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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 No

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Information


Unique identifier OMICS_03702
Name YASS
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

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Publication for YASS

YASS in pipelines

 (9)
2017
PMCID: 5485006
PMID: 28261921
DOI: 10.1111/mec.14084

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

2017
PMCID: 5684833
PMID: 29170674
DOI: 10.3389/fpls.2017.01926

[…] and red denotes ga1 lines., to visualize the structure of the w22 pme repeat region, the 3 mb portion of the chromosome 4 genomic dna sequence containing regions of pme homology was analyzed using yass (noé and kucherov, ) by plotting the sequence against itself (figure 3). genomic sequences of each pme pseudo gene were extracted from the genomic sequence using the genome coordinates produced […]

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 () 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. it contains a core […]

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 () and tandem repeats finder (). a phylogenetic tree was reconstructed using the seaview program ()., the a-genome-specific probe (igs-a) was prepared by digestion […]

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

[…] the high conservation of dif/xercd systems and the possible loss of dif sequences in endosymbionts, with suggestions for other cdr mechanisms []. here, the prediction was based on blast searches and yass alignment [] 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. previous […]


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YASS in publications

 (25)
PMCID: 5910558
PMID: 29678151
DOI: 10.1186/s12864-018-4660-7

[…] analysis []. distributions of aligned reads were visually examined on the integrative genomics viewer [igv v 2.1.21 []] and on the ucsc genome browser. dot matrix analyses were performed using yass [] with default parameters. exon junction heat maps were generated using junction counts normalised to total read counts per sample, and mean expression value of each transcript across samples., […]

PMCID: 5679812
PMID: 29122879
DOI: 10.1128/genomeA.01262-17

[…] of 184,213 subreads, the assembly process using the hierarchical genome-assembly process (hgap) assembly pipeline () resulted in one contig with an 83-fold coverage. this contig was inspected by yass (yet another similarity searcher) () and manually closed using the gepard dotplot generator (), together with the illumina reads and the pilon tool (), and finally oriented to dnaa as the first […]

PMCID: 5684833
PMID: 29170674
DOI: 10.3389/fpls.2017.01926

[…] and red denotes ga1 lines., to visualize the structure of the w22 pme repeat region, the 3 mb portion of the chromosome 4 genomic dna sequence containing regions of pme homology was analyzed using yass (noé and kucherov, ) by plotting the sequence against itself (figure 3). genomic sequences of each pme pseudo gene were extracted from the genomic sequence using the genome coordinates produced […]

PMCID: 5663730
PMID: 29163486
DOI: 10.3389/fimmu.2017.01407

[…] as a gene not identified in the reference loci., multiple sequence alignments were generated using clustalw or muscle in bioeditv7.0.0 and megav6.0 (), respectively. dotplots were generated using yass () with default parameters [scoring matrix for match, transversion, and transition: (5, −4, −3); gap cost (opening): −16; gap cost (extension) −4, window size: 10]. we studied both intraspecies […]

PMCID: 5658505
PMID: 29074667
DOI: 10.1128/genomeA.01196-17

[…] subreads, the assembly process using the hgap assembly pipeline () resulted in one contig with 62-fold coverage. the final contig was inspected manually using the gepard dotplot generator () and yass (), manually closed using illumina reads and the pilon tool (), and oriented to dnaa as the first locus tag. prokka () was used to generate the annotation. blastp searches against the refseq […]


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

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