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install with bioconda Anaconda-Server Badge Anaconda-Server Badge

PfTools

Table of Contents

Foreword

(C) Copyright SIB Swiss Institute of Bioinformatics available from https://github.com/sib-swiss/pftools3 under GPL v2. See LICENSE.

Version 3 contains the original FORTRAN 77 pftools (release 2.3) and the new pftoolsV3 programs.

Installation

Using Docker

First you must have Docker installed and running.
Secondly have a look at the availabe pftools biocontainers at quay.io or at Docker Hub.
Then:

# get the chosen pftools container version
docker pull quay.io/biocontainers/pftools:2.3.5--h4333106_0
 or
docker pull sibswiss/pftools:3.2.8
# use an pftools's tool e.g. pfscan 
docker run quay.io/biocontainers/pftools:2.3.5--h4333106_0 pfscan -h
 or
docker run sibswiss/pftools:3.2.8 pfscan -h

Using Singularity

First you must have Singularity installed and running. Secondly have a look at the availabe pftools biocontainers at quay.io or at Docker Hub.
Then:

# get the chosen pftools container version
singularity pull docker://quay.io/biocontainers/quay.io/biocontainers/pftools:2.3.5--h4333106_0
   or
singularity pull docker://sibswiss/pftools:3.2.8
# run the container
singularity run pftools_2.3.5--h4333106_0.sif

You are now in the container. You can use an pftools's tool e.g. pfscan doing

pfscan -h

Bioconda

conda install -c bioconda pftools

Manually

See here for more information

Prerequisite

  • cmake >= 3.7
  • gcc >= 4.6
  • gfortran (or g77 or f77) for release 2.3 source code
  • perl >= 5.5.3
    • File::Slurp

BUILD

git clone https://github.com/sib-swiss/pftools3.git
cd pftools3
mkdir build
cd build/
cmake ..

COMPILE

make

INSTALL

make install

CHECK/TEST

make test

After installation, in the share/examples/ subdirectory, the test_V3.sh shell script is a good starting point for using pfsearchV3/pfscanV3.

Generalized profile syntax

A description of the generalized profile syntax is given in file:

it was originally published in

  • Bucher P, Bairoch A. A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation. Proc Int Conf Intell Syst Mol Biol. 1994;2:53-61. PubMed PMID: 7584418.

Algorithms description

Technical details about how profiles can be constructed and parametrized are summarized in file:

The very first paper describing the PFTOOLS algorithms is

  • Lüthy R, Xenarios I, Bucher P. Improving the sensitivity of the sequence profile method. Protein Sci. 1994 Jan;3(1):139-46. PubMed PMID: 7511453; PubMed Central PMCID: PMC2142471.

The generalized profile alignment method is closely related to other "classical" algorithm for aligning sequences. For example, it encompasses the Smith-Waterman algorithm and the Viterbi decoding of profile-HMM (as implemented in HMMER2 for example). Relationships between these algorithm were investigated in

  • Bucher P, Hofmann K. A sequence similarity search algorithm based on a probabilistic interpretation of an alignment scoring system. Proc Int Conf Intell Syst Mol Biol. 1996;4:44-51. Review. PubMed PMID: 8877503.

  • Bucher P, Karplus K, Moeri N, Hofmann K. A flexible motif search technique based on generalized profiles. Comput Chem. 1996 Mar;20(1):3-23. PubMed PMID: 8867839.

Relatively detailed explanations about the profile normalized scores, as well as its comparisons with other popular statistics for sequence alignments can be found in

  • Pagni M, Jongeneel CV. Making sense of score statistics for sequence alignments. Brief Bioinform. 2001 Mar;2(1):51-67. PubMed PMID: 11465063.

The heuristic score is succinctly described in

  • Schuepbach T, Pagni M, Bridge A, Bougueleret L, Xenarios I, Cerutti L. pfsearchV3: a code acceleration and heuristic to search PROSITE profiles. Bioinformatics. 2013 May 1;29(9):1215-7. doi: 10.1093/bioinformatics/btt129. PubMed PMID: 23505298; PubMed Central PMCID: PMC3634184.

Applications of the Pftools

Two databases were created based on the PFTOOLS technology: PROSITE and HAMAP and they are still actively maintained

  1. https://prosite.expasy.org/
  2. https://hamap.expasy.org/

The PFTOOLS were initially designed with handling capabilities of DNA sequences. The latest released pfsearchV3 feature support for FASTQ and SAM formats. DNA applications are for example given in

  • Pagni M, Niculita-Hirzel H, Pellissier L, Dubuis A, Xenarios I, Guisan A, Sanders IR, Goudet J, Guex N. Density-based hierarchical clustering of pyro-sequences on a large scale - the case of fungal ITS1. Bioinformatics. 2013 May 15;29(10):1268-74. doi: 10.1093/bioinformatics/btt149. PubMed PMID: 23539304 ; PubMed Central PMCID: PMC3654712.

  • Schmid-Siegert E, Richard S, Luraschi A, Mühlethaler K, Pagni M, Hauser PM. Mechanisms of Surface Antigenic Variation in the Human Pathogenic Fungus Pneumocystis jirovecii. MBio. 2017 Nov 7;8(6). pii: e01470-17. doi: 10.1128/mBio.01470-17. PubMed PMID: 29114024; PubMed Central PMCID: PMC5676039.

Authors

Mas:

  • Philipp Bucher developped the Fortran code
  • Thierry Schuepbach developped the C code

Other contributors:

  • Kay Hofmann
  • Volker Flegel
  • Edouard de Castro
  • Lorenzo Cerruti
  • Marco Pagni
  • Sébastien Moretti
  • Jerven Tjalling Bolleman

SIB Swiss Institute of Bioinformatics Vital-IT Group Quartier Sorge - Batiment Amphipole 1015 Lausanne Switzerland