Yinteraction				10.12.2015

Protein-Protein Interaction Software                                    

Introduction

The program is for analyzing protein-protein interaction in bakery yeast Saccharomyces cerevisiae for predictions of protein pathways and functions. It uses to two databases: 

Tbe Biogrid protein-protein interaction database and the yeast orf-database. 

Both databases are free available (http://thebiogrid.org/, http://www.yeastgenome.org/). 

The program is written in C# on Visual Studio 2012 and the download package: includes the main program, database 1 and 2, help and copyright file. It can be downloaded from http://www.bioinformatics.org. 

Databases 1:

Tbe Biogrid database (BIOGRID-ORGANISM-Saccharomyces_cerevisiae-3.4.126.tab2)

(BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 2006 Jan 1;34) and 

Database 2:

The yeast orf-database (orf_trans_all_R64-2-1_20150113.fasta)

(Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40)

The Biogrid database is a collection of genetic and physical protein-protein interactions. Since the Yinteraction software is using only the genetic interactions and to increase the performance of the program the two databases are shortened to database 1 (extracted from Biogrid) and database 2 (extracted from orf_translation). These databases are provided in the download package and are loaded at the program start. To use future versions of the Biogrid and SGD databases, first download the updated database. Then create and load database1 and 2.  

Component of the main window

1. Menu:

	File: 	Load database 1
		Load database 2
		Quit Program

	Edit	Create database 1
		Create database 2
	
	Analysis Mega Analysis

	Help	Help:  Description of the Program
		About: Short Description and Contributors
		Copyright

2. Results
	Secondary partner
	1/0 secondary, fasta format
	1/0 secondary; tab separated
	Match matrix secondary
	Match count
	1/0 primary; fasta format
	1/0 primary; tab separated
	Match matrix primary
	Dataset


