NetworkBLAST 1.1 usage info:

./networkblast -i <IN> -o <o_prefix> [-d]

Example:
/> ./networkblast -i in -o out

NetworkBlast expects to receive the following input files:
 -i: Specifies prefix for NetworkBlast input files:
  <IN>_params - Parameters file
  <IN>0_int   - PPI data file for species #0
  <IN>1_int   - PPI data file for species #1 (2 species configuration only)
  <IN>_blast  - BLAST data file for species  (2 species configuration only)

 -d: Debug mode: Stop after finding ~%d 1st clusters


^^
The format of parameters file:

# -----------------BEGIN SAMPLE PARAMS FILE------------
no_species 2
beta 0.9
blast_th 1e-30
true_factor0 0.5
true_factor1 0.5
# -----------------END SAMPLE PARAMS FILE------------

Parameters description:
* no_species: Number of species to compare. Legal values: '1' or '2'.
* beta: Probability of an interaction within a complex.
   Higher values (strict mode) result in denser complexes. Range: [0.8..1.0]
* blast_th: E-Value threshold to consider two proteins as sequence similar.
   Range: [10e-100..1e-3]
* true_factor0: FALSE Negatives for species #0. Expected rate of
   missing interactions in the corresponding PPI file. Range: [0..0.8]
* true_factor1: FALSE Negatives for species #1. ditto.


^^
The format for PPI files is as follows:

ID1 ID2 PROBABILITY_OF_INTERACTION
ID3 ID2 PROBABILITY_OF_INTERACTION2
....  

Where ID1, ID3 and ID2 are IDs of species proteins and PROBABILITY_OF_INTERACTION is a weighting percentage from 0-1 of the reliability of connection between the two interactions. The interactions are comutative, e.g. ID1-ID2 is the same as ID2-ID1. The example below demonstrates 5 valid interactions in one protein network with varying degrees of the probability of the connection:

# -------------BEGIN SAMPLE INTERACTION FILE------------

YAL001C YBR123C 0.4489
YAL002W YKR026C 0.4124
YAL002W YLR148W 0.5722
YAL002W YLR396C 0.5211
YAL002W YMR231W 0.5786

# --------------END SAMPLE INTERACTION FILE-------------

If all interactions in a network are to be given equal weighting, then the PROBABILITY_OF_INTERACTION should probably be set near 1.


^^
BLAST data file should be in the format below:

ID1 ID2 EVALUE
ID3 ID4 EVALUE2
...  

Where the first column should relate to species 0 and the second to species 1

For example:

# -----------------BEGIN SAMPLE BLAST VALUES------------

YCR065W CG10002 2e-18
YIL131C CG10002 1e-17
YNL068C CG10002 5e-18
YPR104C CG10002 7e-12
YIL023C CG10006 7e-19
YCR051W CG10011 2e-08
YDR264C CG10011 4e-12
YGR232W CG10011 3e-10
YGR233C CG10011 2e-09
YIL112W CG10011 5e-16

# ------------------END SAMPLE BLAST VALUES-------------


^^
Output files:

<OUT>-network.prop - List of aligned nodes (pair of proteins names separated
 by '|' in 2-speces mode) and complexes IDs the proteins were assigned too.

# ---- SAMPLE ----
network
YLL034C|CG1341 = (63)
YGL048C|CG10229 = (1::37::60::62)
YGL048C|CG7257 = (70::115)
YLR369W|CG5436 = (37::60)
YGR270W|CG6760 = (8::40::100)
YJR017C|CG17051 = (40::113)
# -- END OF SAMPLE --

<OUT>-graph.sif    - Complete alignment graph in .sif (Cytoscape) format.

# ---- SAMPLE ----
YJL008C|CG8439 13 YDL100C|CG1598
YJL008C|CG8439 13 YOR117W|CG5289
YJL008C|CG8439 13 YOR117W|CG4701
YJL008C|CG8439 13 YBR080C|CG1489
# -- END OF SAMPLE --

The file contains lines of form `Y1|F1 yf Y2|F2`, where:
- (Y1, H1) and (Y2,H2) are pairs of sequence similar proteins
  of the species (Yeast and Fly in this example)
- "yf" corresponds to connectivity between proteins Y1,Y2 and F1,F2:
  '3' - not interacting, '2' - dist-2 interacting, '1' - directly interacting.


^^
Utilities:

We supply perl script for splitting NetworkBlast output files to
separate .sif files, containing 1 complex each, which can be
visualized viewed using DualLayer plugin in Cytoscape
(http://www.cytoscape.org/index.php) software.  Script usage example:
/> separate_complexes.pl out-network.prop out-graph.sif


^^
Note:

This specific release of the NetworkBLAST implementation supports
analysis of one network or two networks only. For tools supporting
alignment of three species networks please contact authors.

