YAKUSA statistics

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Associated diseases

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YAKUSA specifications

Information


Unique identifier OMICS_03663
Name YAKUSA
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Requirements
PDB
Source code URL http://wwwabi.snv.jussieu.fr/Yakusa/download/yakusa_src.tar.gz
Maintained Yes

Maintainers


  • person_outline Mathilde Carpentier <>
  • person_outline Sophie Brouillet <>

Additional information


http://wwwabi.snv.jussieu.fr/Yakusa/html/help_general.html

Information


Unique identifier OMICS_03663
Name YAKUSA
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Mathilde Carpentier <>
  • person_outline Sophie Brouillet <>

Additional information


http://wwwabi.snv.jussieu.fr/Yakusa/html/help_general.html

Publication for YAKUSA

YAKUSA in publications

 (9)
PMCID: 5331158
PMID: 28280526
DOI: 10.1016/j.csbj.2017.01.011

[…] (sw) algorithm for local sequence alignment , with implementation available in the r package biostrings;•tm-align , available at http://zhanglab.ccmb.med.umich.edu/tm-align/;•yakusa , available at http://bioserv.rpbs.jussieu.fr/yakusa/download/index.html;•dali , available at http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads/v3/., needleman–wunsch (nw) algorithm […]

PMCID: 4702403
PMID: 26732380
DOI: 10.1186/s12859-015-0866-8

[…] s4)., the representative set of 100 protein queries was compared against the astral 2.03 40 % sequence identity dataset (which contains a total of 11,121 domains; for details see ) with sheba, yakusa, qp tableau search, gangsta+, structal, topmatch and moma computer programs. the performance of these methods was assessed by roc curve analysis based on the normalized scores reported […]

PMCID: 3583823
PMID: 23157331
DOI: 10.1186/1471-2105-13-307

[…] compare protein domain structures at the level of residues and sometime even atoms, to detect structural similarities with high sensitivity and accuracy. for example, carpentier et al. proposed yakusa [] which compares protein structures using one-dimensional characterizations based on protein backbone internal angles, while jung and lee proposed sheba [] for structural database scanning […]

PMCID: 3534633
PMID: 22974051
DOI: 10.1186/1471-2105-13-233

[…] to apply to the reduced graph a standard graph clustering algorithm. such method was used for classifying astral-40 non-redundant protein domains, identifying significant pairwise similarities with yakusa, a program devised for rapid 3d structure alignments., we show that filtering similarities prior to standard graph based clustering process by applying ternary similarity constraints i) […]

PMCID: 3183006
PMID: 21923949
DOI: 10.1186/1756-3305-4-178

[…] the prevalence appears to vary within regions and across the country (figure ). the review by sasa [], cites the absence of w. bancrofti in night blood surveys from pawa, haut-uele province [], and yakusa, oriental province [], and highlights that these authors state that w. bancrofti was never confirmed with precision from the congo, and contrary to belief it was considered not to extend […]


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YAKUSA institution(s)
Atelier de BioInformatique, Paris, France

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