News

Coming Soon!

March 10, 2017

Users will be able to visualize CHO cell mRNA expression data either from published DNA-microarray or RNA-Seq experiments via JBrowse. The visualized data will enable users to easily obtain gene expression levels and compare gene expression levels among different conditions.

CHOmine (BETA-Version)

August 19, 2016

CHOmine, the InterMine site for CHO and Chinese hamster, went online on August 11, 2016 at https://chomine.boku.ac.at/. CHOmine collects and integrates publicly available Chinese hamster and CHO data, where different datasets are connected to provide user-friendly access. Currently, users are asked to test the site and to provide feedback (impressions, comments, issues, and suggestions for improvements) to Matthias.Gerstl@acib.at or Nicole.Borth@boku.ac.at.

CHO Epigenomic Data

April 14, 2016

A new database of epigenomic information (cho-epigenome.boku.ac.at) for 6 CHO cell lines has been created by Dr. Nicole Borth's group. A link to this database has been added to CHOgenome.org's Data webpage. The epigenomic database website hosts genome sequences for 6 cell lines, SNPs, structural variants, full genome methylation data, and batch culture histone modification data. The manuscript describing the acquisition and analysis of the data can be found here.

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BLAST Tutorial

August 2014, Version 2.0

CHOgenome.org BLAST is adapted from ViroBLAST version 2.2.

To start a BLAST search, complete all of the required parameters:

Copy and paste one or multiple query sequences in FASTA format to the text box, or upload a sequence file in FASTA format.

Choose a BLAST program and select the database(s) to BLAST against. Multiple databases may be selected by holding the 'Ctrl' key and highlighting each of the appropriate databases.

Optional: Change the other default search parameters to get more specific results.

Click "BLAST" button to start search.

Screenshot 1

The output is user-friendly, as it is easy to navigate the BLAST results.

The user can modify the default search parameters to filter the BLAST results.

Screenshot 2

Clicking one of the "Subject" field links will link to the NCBI GenBank report of the subject sequence.

Screenshot 3

Clicking one of the "Bit_Score" field links will show the pair-wise alignment between the query sequence and the respective BLAST result subject sequence.

Screenshot 4

Clicking the "Full BLAST Report" buttons [Examine/Download] will either open or download the BLAST result files, respectively. ViroBLAST automatically provides links to each query sequence BLAST result for the convenience of analysis of results. ViroBLAST also automatically divides large output files into several smaller files, which allows users to download the files quickly and easily.

Screenshot 5

Check the subject sequences you want to be downloaded or check the "Download all sequences" box in the "Subject (hit) sequences" field and click the "Download" button to download aligned sequences to your local computer.

Screenshot 6