README

Copyright (C) 2015 Leibniz Institute for Natural  Product  Research  and
Infection Biology -- Hans-Knoell-Institute (HKI)

This program comes with ABSOLUTELY NO WARRANTY. This is  free  software,
and you are welcome to redistribute it under certain conditions. See the
file COPYING, which you should have received along  with  this  program,
for details.

     ##############################################################
     # SMIPS - (S)econdary (M)etablolites from (I)nter(P)ro(S)can #
     ##############################################################

SMIPS is  a  tool  to  predict  secondary  metabolite  (SM)  anchor  (or
backbone) genes in protein sequences. These enzymes play a major role in
synthesizing secondary metabolites and their genes are  often  clustered
together with others participating in the same metabolic pathway. Common
SM anchor genes are Polyketide synthases (PKS) and Non-ribosomal peptide
synthetases  (NRPS).  The  predictions  are  based  on  protein   domain
annotations provided by InterProScan.


usage: smips.pl [ options ] [ <interproscan_file.[tsv|out|tab]> | <protein_sequences.fasta> ]

options:

   --path-to-interproscan, -p <path>

        Path to InterProScan software, including the file name.  Usually
        the file name is "interproscan.sh". If not specified, SMIPS uses
        the "which" command to figure out the location of  InterProScan.
        Only needed if a FASTA file is given.


SMIPS accepts one (many) InterProScan  output  file(s)  in  TSV  or  OUT
format, or the corresponding JGI files  in  TAB  format,  as  input.  It
analyses them for typical SM  anchor/backbone  genes  and  writes  their
domain structure, along with additionl information, to two files in  CSV
format, extending the file name(s) of the input file(s).

As an alternative, SMIPS accepts protein sequence files in FASTA format.
If  InterProScan  is  installed  on  your  machine,  SMIPS  first  calls
InterProScan with the given FASTA file(s) and  than  proceeds  with  the
resulting TSV file(s).

If you don't have a proper InterProScan output at hand, you may download
and install InterProScan from

   http://www.ebi.ac.uk/interpro/download.html

and apply the following command-line to get the desired file (SMIPS will
apply the very same command-line, if you run it with a FASTA file)

   interproscan.sh -appl PrositePatterns,SuperFamily,PfamA,SMART,TIGRFAM -i <fasta file with protein sequences> -f tsv,html -iprlookup


These mappings inside the SMIPS' source code are used to assign  protein
domains and anchor genes to this or that category (change them,  if  you
like):

InterPro IPR ID => Anchor gene domain type (%iprs variable):
{
  'IPR000537' => 'Prenyltransferase',
  'IPR000873' => 'A',
  'IPR001031' => 'TE',
  'IPR001242' => 'C',
  'IPR003231' => 'PP',
  'IPR004033' => 'MT',
  'IPR004568' => 'PP',
  'IPR006162' => 'PP',
  'IPR006765' => 'Cyc',
  'IPR008278' => 'PP',
  'IPR009081' => 'PP',
  'IPR010060' => 'xNRPS',
  'IPR010071' => 'A',
  'IPR010080' => 'TE',
  'IPR011032' => 'ER',
  'IPR012148' => 'Prenyltransferase',
  'IPR012728' => 'xNRPS',
  'IPR013149' => 'ER',
  'IPR013154' => 'ER',
  'IPR013216' => 'MT',
  'IPR013217' => 'MT',
  'IPR013601' => 'xPKS',
  'IPR013624' => 'xNRPS',
  'IPR013968' => 'KR',
  'IPR014030' => 'KS',
  'IPR014031' => 'KS',
  'IPR014043' => 'AT',
  'IPR015083' => 'xPKS',
  'IPR016035' => 'AT',
  'IPR016036' => 'AT',
  'IPR017795' => 'Prenyltransferase',
  'IPR017796' => 'Prenyltransferase',
  'IPR018201' => 'KS',
  'IPR020801' => 'AT',
  'IPR020802' => 'TE',
  'IPR020803' => 'MT',
  'IPR020806' => 'PP',
  'IPR020807' => 'DH',
  'IPR020841' => 'KS',
  'IPR020842' => 'KR',
  'IPR020843' => 'ER',
  'IPR020845' => 'A',
  'IPR025110' => 'A',
  'IPR029063' => 'MT'
}

Anchor gene domain type => Anchor gene type (%domains variable):
{
  'A' => 'NRPS',
  'AT' => 'PKS',
  'C' => 'NRPS',
  'Cyc' => 'PKS',
  'DH' => 'PKS',
  'ER' => 'PKS',
  'KR' => 'PKS',
  'KS' => 'PKS',
  'MT' => 'PKS/NRPS',
  'PP' => 'PKS/NRPS',
  'Prenyltransferase' => 'DMATS',
  'TE' => 'PKS/NRPS',
  'xNRPS' => 'NRPS',
  'xPKS' => 'PKS'
}


Contact: gianni.panagiotou@leibniz-hki.de, thomas.wolf@leibniz-hki.de