hurwitzlab/ProphET

Name: ProphET

Owner: Hurwitz Lab

Description: null

Forked from: jaumlrc/ProphET

Created: 2017-10-21 16:25:36.0

Updated: 2017-10-21 16:25:38.0

Pushed: 2017-08-22 14:04:25.0

Homepage: null

Size: 25809

Language: Perl

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README

ProphET, Prophage Estimation Tool: a standalone prophage sequence prediction tool with self-updating reference database.

João L. Reis-Cunha^1,2, Daniella C. Bartholomeu², Ashlee M. Earl¹, Bruce W. Birren¹, Gustavo C. Cerqueira¹

Manuscript draft in BioRxiv

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¹ Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States

² Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil

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Contact

jaumlrc@gmail.com

gustavo@broadinstitute.org

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Required libraries and programs:

Broad users don't need to install any of the of programs and libraries listed below. If you are Broadie please follow the instructions on README_BROAD_USERS.md before installing and running ProphET.

• EMBOSS suite

• BEDTools suite

• BLAST

• Perl module Bio::Perl

• Perl module SVG

• Perl module GD

• Perl moduel GD::SVG

• Perl module Bio::Graphics

• Perl module LWP::Simple

• Perl module XML::Simple

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ProphET installation:

To either install ProphET or to update ProphET bacteriophage database please execute the following command from ProphET's home directory:

INSTALL.pl

This will search for required libraries, set the paths of required programs and download from Genbank (NCBI) all genomes associated to 16 families of bacteriophages (listed in config.dir/Prophages_names_sem_Claviviridae_Guttaviridae-TxID ).

Some warnings will be issued during the setup of ProphET DB. See some examples below:

ing: bad /anticodon value '(pos:complement(13054..13056),aa:Met,seq:cat)'
ing: NC_022920: Bad value '(pos:complement(13054..13056),aa:Met,seq:cat)' for tag '/anticodon'

Those warnings refer to unexpected format for coordinates of tRNA features and they won't affect the execution.

If the script fails and reports missing Perl modules/libraries, please folow the instrucions on file README_INSTALLING_PERL_MODULES.md on how to install those.

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Testing installation:

From ProphET's home directory execute the following command:

ProphET_standalone.pl --fasta test.fasta --gff_in test.gff --outdir test

The execution should take ~ 5 minutes.

Three putative prophages should be reported and its coordinates indicated in the file test/phages_coords:

AT:
ffold>  <#prophage> <genomic.start.coord> <genomic.end.coord>

ENT:
05362.1     1       327710  378140
05362.1     2       1292553 1330556

The nucleotide sequence of each prophage can be found in:

/NC_005362.1.phage_1.fas
/NC_005362.1.phage_2.fas

The program also renders a simple diagram depicting all coding genes in the bacterial genome, coding genes with significant matches to phage genes and the location of predicted prophages:

/NC_005362.1.svg

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Before running ProphET in your favorite bacterial genome

• Check if the GFF file that will be provided to ProphET has the format specified by The Sequence Ontology Consortium

• Check if all sequences IDs in the FASTA file (header of each sequence) matches perfectly the source field in the GFF file (first column of the GFF) and vice-versa.

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Usage:

ProphET_standalone.pl --fasta_in <file> --gff_in <file> --outdir
<string> [--grid] [--gff_trna <file> ] [--help]

ons:
--fasta_in - Bacterial genome Fasta file

--gff_in - Bacterial GFF file

--gff_trna - Optional parameter, in case the tRNAs are reported in a
separate GFF please provide it here <(Optional)>

--outdir - output directory

--grid - Use UGER for BLAST jobs (Currently only works in the Broad
Institute UGER grid system) (Optional)

--help - print this and some additional info. about FASTA and GFF input
format (Optional)