genomemap Files

Release notes for genomemap application version 1.1.0

Date: Sep 7, 2012

Project website: http://genomemap.sourceforge.net

The following new features have been added.

1. Data support. Jobs can select data from a drop-down combo box. Only relevant data sets are shown. The application is preloaded with data sets.

2. Likelihood computation for TAB08 & KSA00

3. Contig maps for KSA00 data

4. Repeats map for OrganismData


The following is the list of all supported jobs, prefixed by the release in which they appear, in descending order.

1.1.0 Lhood TAB08: (Category: Likelihood Computations)

Computes data likelihood for the genetic map model TAB08.


1.1.0 Lhood KSA00: (Category: Likelihood Computations)

Computes data likelihood for the genetic map model TAB08.


1.1.0 Contig Map: (Category: Draw Maps)

Draws FULL and MINIMAL contig maps for the physical map data from model KSA00.


1.1.0 Repeats Map: (Category: Draw Maps)

Draws clone repeats distribution map across the genome using OrganismData.

1.0.0 ProcessComplData: (Category: Organism Data)

From an unorganized assignment data format (known as complementation data) create the assignment.xml file. The complementation data has the Java properties file format, where the key is a gene label and the value is the assigned clone labels, separated by comma. The feature organizes the complementation data into the format assignment.xsd and creates an instance. The format of assignment.xsd uses an instance of OrganismData for this purpose. The feature only recognizes the genes and clones present in the instance of OrganismData and ignores the rest while processing the complementation data.

This feature has been used as a part of the process of creating the assignment data for data 1.0. Version 1.0 indicates a specific collection of raw data in a certain format. Some complementation data was available from Dr. Arnold (arnold_compl_data.txt) and some was generated using data from the Broad website (broad_compl_data.txt). These two were merged manually in a file (all_compl_data.txt) and the file was run with this feature to produce the global assignment data (assignment.xml). The instance of OrganismData used was created by the provider 'impl1'. Note that a the result of a provider is always reproducible i.e., it uses onyl deterministic steps (no probabilistic missing value algorithms are used). A provider uses a certain  format of the data and uses specific algorithms to clean the data. However, the specific version of the data (i.e., the URL of the data 1.0) and its linkage groups to be used are configurable. The linkage groups to be used can be specified by a comma separated list of the available linkage groups. For our analysis we used the URL 'organism_data_impl1' and all the available linkage groups (1,...,7).



1.0.0 ClassifyGenes: (Category: Organism Data)

This feature was used as a part of the process of creating the assignment data for data 1.0. To collect the complementation data from Broad, we needed to manually collect the clone assignments for all the genes in data 1.0. From all the genes available on the Broad website we needed to find the genes available in data 1.0, organized by the linkage groups. This feature was used exactly for this purpose. We created a list of all the gene names and ran it through this feature to find the desired genes. 

Clone labels have different formats in Broad and Arnold data and this feature does not recognize gene and clone labels in the complementation data if they do not match to that of the OrganismData instance used. To that end, we needed to check (check_broad_clone_names.groovy) and convert (convert_broad_clone_names.groovy) the clone labels.