[ensembl-dev] Ensembl Compara genomic_align/genomic_align_block Table

Javier Herrero jherrero at ebi.ac.uk
Fri Jun 15 08:54:28 BST 2012

Dear Will

We have moved level_id from the genomic_align to the genomic_align_block 
table. This value is used for the lastz-net alignments. One particular 
net represents a set of chains that are in the same order and 
orientation. The main nets are on level 1. In the gaps left between the 
chains, you can sometimes find other chain and use them to define 
smaller nets. You can think of those like an insertion in a long 
syntenic block. These secondary nets are on level 2. You can find more 
complex structures, resulting in nets in deeper levels. You can set the 
value to 1 if level_id is not relevant in your case.

node_id is a link from genomic_align to genomic_align_tree. It is used 
for the EPO multiple alignments, where we use a tree to relate the 
sequences. If you don't use genomic_align_trees, you can leave this as a 

Visible has been added to better handle self-alignments. When building 
self-alignments, you can get redundant alignments. We use this flag to 
handle those cases and make sure the API returns what you expect. If you 
don't use self-alignments, you can set all the visible flags to true (1).

Kind regards


On 14/06/12 16:27, Will Chow wrote:
> Hi Dev'rs,
> I noticed two new columns to the Compara genomic_align tables, "visible" and "node_id" and for genomic_align_block there is "level_id".  As the table structure says these can't be null (node_id is ok), can someone tell me what they are for?
> cheers
> Will
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Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

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