Protocols

PAMES specifications

Information


Unique identifier OMICS_25842
Name PAMES
Alternative name Purity Assessment from clonal MEthylation Sites
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.2.0
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Francesca Demichelis
  • person_outline Matteo Benelli

Publication for Purity Assessment from clonal MEthylation Sites

PAMES citations

 (2)
call_split

Heterogenous Distribution of MTHFR Gene Variants among Mestizos and Diverse Amerindian Groups from Mexico

2016
PLoS One
PMCID: 5029802
PMID: 27649570
DOI: 10.1371/journal.pone.0163248
call_split See protocol

[…] analyses, with PLINK software, v1.07 []. Significant differences were defined as P<0.05. For further allele frequency comparisons between MAs and MEZs by geographical regions, we excluded Seris (N), Pames (CE), Huaves (S), and Tojolabales (SE) because they fulfilled at least two of the following three criteria: a) in previous studies, they were reported as genetically divergent from all other eth […]

library_books

CRISPR spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR Cas I E variants of Escherichia coli

2013
RNA Biol
PMCID: 3737337
PMID: 23445770
DOI: 10.4161/rna.24023

[…] to be equally oriented with respect to the PAM. Moreover, this conservation in orientation applies to the CRISPR-Cas type: spacer ends equivalent to the protospacer edges adjacent to the PAM (termed PAMEs) of CRISPR-Cas type I are oriented toward the leader.,,, This implies that acquisition proteins (Cas1 and/or Cas2) together with element(s) at the spacer integration region (either the leader an […]

PAMES institution(s)
Centre for Integrative Biology, University of Trento, Trento, Italy; Bioinformatics Unit, Hospital of Prato, Istituto Toscano Tumori, Prato, Italy
PAMES funding source(s)
Supported by the NCI R01CA125612-05A1 and by European Research Council ERCCoG648670.

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