Here are the steps for making queries with pre-loaded data:
- Select the data source you wish to use by clicking on the corresponding tab. The details of the data sources are given below.
- On the server, select the genomes you want to work with by checking the box next to each genome. (You may choose two or more genomes).
- Click Start button.
- In the following page, you have three different queries.
- Choose one of the queries and proceed.
- The next page shows you the output of your query.
- You may modify the parameters and update your result.
Here is the list of tools on the server which you may use.
Pre-loaded data sources
The data of orthologs (or sequence tags) may be obtained from multiple sources; the difference stems from the procedure followed to obtain the orthologs. Cinteny makes available data from the following sources. A user may upload his own data or request us to upload other standard databases.
HomoloGene
HomoloGene is part of the NCBI Entrez suite, "it is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes".
The build procedure may be found here: HomoloGene build procedure
RoundUp
"Roundup Orthology Database is a large-scale database of orthology covering over 250 publicly available genomes".
The build procedure may be found here: Roundup Orthology Database
Grimm
Human, mouse and rat conserved sequence tags used by Pavel Pevzner's group. For details visit Human-mouse-rat alignments page
Bacteria - RoundUp
Bacterial orthologs from the RoundUp database.