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I know that Informatica is a software that extract data from data sources (database or flat file) and convert them to the same data types respectively so it will be easier for the source definition to map and load data to the target definition (database or flat file). What if the source definition and the target definition are loaded with different tables like (Like tables without the same columns) will it still work?

I have a few questions regarding to informatica..

Informatica :

 Source Definition - Upload data from a flat file or data from tables in the database
 Source Qualifier - It is normally created with the source definition which is to be used to manipulate the imported data to match with the data type in informatica, which later to be linked with the target definition.
 Target Definition - It is created to store the only filtered columns needed for the target structure.
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Not sure what is the question here. Could you please go through the Informatica documentation more? This is an Extract, Transform, Load tool that can read,modify,load anything ranging from flat file, xml, wsdl, hive, RDB to cloud. So if you ware wondering if number of fields arent same or their datatype, length arent same, you can relax. - Koushik Roy
yes, source tables and target tables don't need to have anything in common. They may have a whole fleet of transformations between them. - access_granted
Imagine you can have a list of customers in a table, as a source - and as target an average number of customers per city. The target can be anything that can be created out of the source in some process of transforming the input. ETL is not just about copying data - the 'T' in ETL stands for 'Transform' and can mean any (sometimes very complex) transformations. - Maciejg

2 Answers

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Short answer: YES

That is why we have Informatica. To transform data from different sources to be transfered to different targets. 
e.g.   
from file to oracle_db.
from oracle_db to mysql. etc
from oracle_db to csv file and to email attachment etc

Example: Data from different sources to one target

enter image description here

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Yes, it will still work if your source columns and target columns are different. Lets assume that Source table is containing 4 columns (such as id, name, age, address) and Target is getting the columns as (identity, title, age_group, salary) where the title and salary columns were derived with the help of Primary key-foreign key constraint.