Usage

ShadowCaster uses a configuration file (args.ini) to manage all the options needed. This file must be specified on the command line and will supply the following arguments:

Files

  • Query genome Only fasta files.
  • Query proteome Only fasta files
  • OrthoMcl configuration file, previously obtained with the installation of OrthoMcl-pipeline(orthomcl.conf). This file looks like:
coOrthologTable=CoOrtholog
dbConnectString=dbi:mysql:orthomcl:localhost:mysql_local_infile=1
dbLogin=orthomcl
dbPassword=orthomcl
dbVendor=mysql
evalueExponentCutoff=-5
inParalogTable=InParalog
interTaxonMatchView=InterTaxonMatch
oracleIndexTblSpc=NONE
orthologTable=Ortholog
percentMatchCutoff=50
similarSequencesTable=SimilarSequences

Path

  • Proteomes folder, contain the proteomes(Only fasta files) of each species to construct the shadow.

    -Provided by the user (a collection of FASTA files)

    or

    -Automatically retrieved by ShadowCaster from the NCBI ftp site by using script/get_proteomes.py, see get_proteomes.py.

  • Blastp26 ShadowCaster uses blastp 2.2.26, specify the binary file or the shell command used

  • Formatdb Specify the binary file or the shell command used. Ex. formatdb

Parametric

  • nuSVM A bound between the fraction of training errors and the fraction of support vectors. Should be in the interval (0, 1].

A template of the args.ini file can be found in the bin folder.

Specifications of fasta files

The id of each gene in the GENOME fasta file SHOULD not contain any character like |, #, %, /, \, *, &, $, !, :. It is preferred only one identification number.

All the proteomes files provided by the user MUST follow these specifications:
  • Fasta file name ONLY can be the binomial name of the species (Rhodanobacter_denitrificans.fasta).
  • Each id record of a fasta file MUST have only one id number or the following structure:
>AGG91012.1 ribosomal protein L34 [Rhodanobacter denitrificans]
MKRTFQPSKLKRARTHGFRARMATADGRKVLNARRAKGRKRLIP

Examples of the input files can be found in the test data repository of ShadowCaster, see here

Run ShadowCaster

cd $ShadowCaster/bin/
shadowcaster --config_file args.ini