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Protocols

PFAAT specifications

Information


Unique identifier OMICS_08907
Name PFAAT
Alternative name Protein Family Alignment Annotation Tool
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 2.0
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Daniel R Caffrey

Publications for Protein Family Alignment Annotation Tool

PFAAT citations

 (11)
library_books

Mapping the malaria parasite druggable genome by using in vitro evolution and chemogenomics

2018
PMCID: 5925756
PMID: 29326268
DOI: 10.1126/science.aan4472

[…] selection in clinical isolates. Mutations in 3247 clinical P. falciparum isolates reveal that four mediators of resistance (the ABC transporter gene pfabcI3, the putative amino acid transporter gene pfaat2, the AP2 transcription factor gene pfap2tf-6b, and the farnesyltransferase gene pfftb) have nonsynonymous-to-synonymous ratios greater than 2:1, suggesting that they are under positive selectio […]

library_books

Predicting phenotype from genotype: Improving accuracy through more robust experimental and computational modeling

2017
Hum Mutat
PMCID: 5516182
PMID: 28230923
DOI: 10.1002/humu.23193

[…] , blast results were required to be at least 75% the length of the ADRB2 query sequence. The resulting homolog list was aligned using MUSCLE (Edgar, ) and the neighbor‐joining tree was extracted with PFAAT (Caffrey et al., ) using percentage identity of all columns for all sequences. In reference to the initial query sequence, this tree was pruned into a smaller subdivision encompassing only close […]

library_books

IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments

2015
Evol Bioinform Online
PMCID: 4362671
PMID: 25861209
DOI: 10.4137/EBO.S18980

[…] lyze MSAs. Presently, a lot of MSA editing and analyzing tools are available. The popular and widely used tools include Jalview, SeaView, MEGA, STRAP, PFAAT, Base-by-Base, and CINEMA. Jalview, STRAP, PFAAT, and Base-by-Base are Java programs, whereas SeaView, MEGA, and CINEMA are written in C++ language. Results showed that MSApad loaded more than 50,000 sequences with a sequence length of 2,696 b […]

library_books

The repertoire of G protein coupled receptors in the human parasite Schistosoma mansoni and the model organism Schmidtea mediterranea

2011
BMC Genomics
PMCID: 3261222
PMID: 22145649
DOI: 10.1186/1471-2164-12-596

[…] th (TM > 5) receptors were first processed for removal of the N- and C-termini. ClustalX 2.0 [] was used to generate multiple sequence alignments of the GPCRs to be examined, with default parameters. PFAAT [] was used to edit the resulting alignment with attention to key motifs and residues housed within transmembrane domains. Low-entropy sequence blocks present in all sequences were retained. The […]

library_books

Using Shifts in Amino Acid Frequency and Substitution Rate to Identify Latent Structural Characters in Base Excision Repair Enzymes

2011
PLoS One
PMCID: 3188539
PMID: 21998646
DOI: 10.1371/journal.pone.0025246

[…] FFT and ASH were used, with high accuracy parameters (iterative refinement incorporating local alignment information for the alignment), to align the sequences based on crystal structures , , , , . PFAAT was used for visualization of the sequence alignment and Seaview was used to remove phylogenetically uninformative sites. Neighbor-joining phylogenetic trees were constructed using PHYLIP PRO […]

library_books

Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence associated proteins

2010
BMC Genomics
PMCID: 2890568
PMID: 20537180
DOI: 10.1186/1471-2164-11-369

[…] e sequences of the orthologs were collected in fasta format from the UniProt database. Alignments were carried out using the L-INS-I method of the MAFFT software, version 6.713 [] and evaluated using pfaat []. Maximum likelihood trees were inferred using the Treefinder software []. The Whelan and Goldman substitution model [] was used. […]

Citations

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PFAAT institution(s)
Pfizer Discovery Technology Center, Cambridge, MA, USA; Neogenesis Drug Discovery, Cambridge, MA, USA

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