[ensembl-dev] Ensembl Compara genomic_align/genomic_align_block Table

[Will Chow]

Cheers Javier.


On 15 Jun 2012, at 08:54, Javier Herrero wrote:

> 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 NULL.
> 
> 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
> 
> Javier
> 
> 
> 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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