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Pftools specifications

Information


Unique identifier OMICS_29588
Name Pftools
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format PSA, XPSA
Operating system Unix/Linux
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

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Pftools citations

 (20)
call_split

A Novel Small RNA Regulates Tolerance and Virulence in Shigella flexneri by Responding to Acidic Environmental Changes

2016
PMCID: 4782007
PMID: 27014636
DOI: 10.3389/fcimb.2016.00024
call_split See protocol

[…] Given that sRNAs are mainly located in the intergenic regions of the genome, we predicted the promoter and terminator in the intergenic regions of Shigella flexneri. The profile search program pftools2.3 (Lesnik et al., ) was used for promoter prediction, and RNAMotif (Berg and von Hippel, ; Livny et al., ) was used for rho-independent terminator prediction. Only the intergenic regions with […]

library_books

Identification of a Novel Small Non Coding RNA Modulating the Intracellular Survival of Brucella melitensis

2015
Front Microbiol
PMCID: 4365724
PMID: 25852653
DOI: 10.3389/fmicb.2015.00164

[…] cific and thus exclude from further analyses. The replication origin, putative pseudogenes, and intergenic sequences encoding tRNAs or rRNAs were also excluded. Promoters were identified in IGRs with pftools 2.3 with a cut-off value of 255, while terminators were identified using RNAMotif (Lesnik et al., ). Motif descriptor came from sRNAPredict (Waldor Lab, Tufts University). IGRs with both promo […]

library_books

Statistical Approaches to Detecting and Analyzing Tandem Repeats in Genomic Sequences

2015
Front Bioeng Biotechnol
PMCID: 4362331
PMID: 25853125
DOI: 10.3389/fbioe.2015.00031

[…] nnotation typically relies on sequence profile hidden Markov models (HMMs). Circular connections in an HMM allow the annotation of full TR units (Bucher et al., ; Schaper et al., ), as implemented in pftools (Sigrist et al., ) and in our Python TR Annotation Library TRAL (http://elkeschaper.github.io/tral/). General profile HMM annotation can be used to detect TR units [e.g., HMMER; Eddy ()], but […]

call_split

Evolutionary link between metazoan RHIM motif and prion forming domain of fungal heterokaryon incompatibility factor HET s/HET s

2014
Sci Rep
PMCID: 4262963
PMID: 25500536
DOI: 10.1038/srep07436
call_split See protocol

[…] d.mit.edu) and the DOE joint Genome Institute (http://www.jgi.doe.gov) using the PHYTOZOME and MYCOCOSM portals. Sequence database searches were performed by the generalized profile method, using the pftools package. Generalized profiles were constructed using the BLOSUM45 substitution matrix and default penalties of 2.1 for gap opening and 0.2 for gap extension. The statistical significance of pr […]

library_books

Developing eThread Pipeline Using SAGA Pilot Abstraction for Large Scale Structural Bioinformatics

2014
Biomed Res Int
PMCID: 4066679
PMID: 24995285
DOI: 10.1155/2014/348725

[…] volume could be added.In , we compare experimental results using SAGA-Pilot and estimated ideal limits using the same 20 sequences out of 110 benchmarks (see for the results with 110 sequences with pfTools). The ideal limit is the time when the benchmark time-to-solution of 20 sequences is divided by the number of cores. The difference shows how the simple parallel implementation using the defau […]

call_split

Unleashing the power of meta threading for evolution/structure based function inference of proteins

2013
Front Genet
PMCID: 3686302
PMID: 23802014
DOI: 10.3389/fgene.2013.00118
call_split See protocol

[…] To identify functional templates, we use eThread (), which integrates ten state-of-the-art protein threading/fold recognition algorithms: CSI-BLAST (), COMPASS (), HHpred (), HMMER (), pfTools (), pGenThreader (), SAM-T2K (), SP3 (), SPARKS2 (), and Threader (). eThread was originally design to detect structural templates using machine learning and a set of feature vectors composed […]

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