main
Class BLM

java.lang.Object
  extended by main.BLM

public class BLM
extends java.lang.Object

A Java Program for solving bounded-list network querying problems. The input is specified as follows
A list of complexes, that is, subsets of vertices of G who should be queried in H
A graph G (that contains the query)
A graph H (the pattern)
A list of similarities between vertices in G and H
A similarity threshold t, for considering vertices in G and H similar.

For each complex C in the complex list, the program finds (if it exists) a subnetwork of H that is similar to the subnetwork G[C] of G that is induced by C. Herein, similarity has two "components": First, we want to map each vertex in C only to a similar vertex in H (similarity is specified by the similarity file and the similarity threshold p). Second, the topology of the graph that is induced by the matching should be similar to the topology of G[C].

The following options are available for considering subnetworks as similar:
Injective Homomorphism - asks for a mapping from the vertices in G[C] to the vertices in H that is an injective homomorphism . That is, for two vertices that are adjacent in G[C], the matches have to be adjacent in H.
Subgraph Isomorphism - asks for a mapping from the vertices in G[C] to the vertices in H
that is an isomorphism. That is, it is a mapping from C to a vertex set S (from H), that is an isomorphism from G[C] to H[S]. You should have received the following example data with this program.
- two protein interaction networks, one with yeast proteins, one with human proteins
- a list of human protein complexes
- a file that contains sequence similarities for yeast and human proteins

When using this data, please cite the following publication:
Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan: Topology-Free Querying of Protein Interaction Networks. RECOMB 2009: 74-89

Source: http://ftp.akt.tu-berlin.de/BLM
For questions, remarks etc., please send an e-mail to Christian Komusiewicz (christian.komusiewicz@tu-berlin.de)

Version:
0.1
Author:
Christian Komusiewicz

Constructor Summary
BLM()
           
 
Method Summary
static void main(java.lang.String[] args)
          Main method of the Bounded List Morphism Program, supplies different algorithms for solving the Bounded List Morphism problem for two graphs.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BLM

public BLM()
Method Detail

main

public static void main(java.lang.String[] args)
                 throws java.io.IOException
Main method of the Bounded List Morphism Program, supplies different algorithms for solving the Bounded List Morphism problem for two graphs.

Parameters:
args - - A string array that contains paths to the input files and further options. It should contain the following, in the same order:
1) A Path to the complex file. Each line of the file should consist of a complex in the following format:
Complex Name \t Protein1 \space Protein2
2) A Path to the graph that contains the query, each line representing an edge: Protein_1 \space Protein_2
3) A Path to the host, in the same format as above
4) A Path to the similarity file. Each line specifies a similarity, given by BLAST E-values between two proteins: Protein_1 \space Protein_2 \space E-value 5) Sets the output path for the reported matches
The following arguments are optional, each has a default value
6) Sets the E-value threshold for orthology; default value is 1E-7 7) Sets the mapping option; default is Injective Homomorphism; "2" is Subgraph Isomorphism 8) Sets the minimum size for reporting matches; default minimum size is 3 9) Sets the algorithm option; default is the iterative algorithm; "2" is the search tree algorithm
Throws:
java.io.IOException