[ensembl-dev] question about compara in plants

[Eduardo Andrés León]

Dear all,
	I usually got  some alignments in mammals using the method_link_species_set :

	my $method_link_species_set = $method_link_species_set_adaptor->fetch_by_method_link_type_species_set_name("EPO", "mammals");

Now I,m working in a new project to do something similar but in Arabidopsis thaliana. 

The EPO and mammals words,  I know that they come from the name field, in the table method_link_species_set  :

mysql> use ensembl_compara_66
mysql> select name from method_link_species_set where name like '%mammals%';
+--------------------------------------------------+
| name                                             |
+--------------------------------------------------+
| 12 eutherian mammals EPO                         |
| 35 eutherian mammals EPO_LOW_COVERAGE            |
| Gerp Constrained Elements (35 eutherian mammals) |
| Gerp Conservation Scores (35 eutherian mammals)  |
+--------------------------------------------------+
4 rows in set (0.00 sec)

But in plants the thing is quite different :

mysql> use ensembl_compara_plants_13_66 -A
mysql> select name from method_link_species_set where name like '%orthologues%';
+-----------------------+
| name                  |
+-----------------------+
| 1245-1173 orthologues |
| 1505-1245 orthologues |
| 1505-1173 orthologues |
| 1505-1506 orthologues |
| 1245-1506 orthologues |
| 1173-1506 orthologues |
| 1505-1537 orthologues |
| 1245-1537 orthologues |
| 1173-1537 orthologues |

.....

So what do I have to use in order to get the alignments from the arabidopsis taxa ? http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=3701&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=5&unlock
What are those numbers in the name description ?

by the way , the documentations for the API's in plants are not working :


http://plants.ensembl.org/info/docs/Doxygen/compara-api/index.html
http://plants.ensembl.org/info/docs/Doxygen/core-api/index.html

Thanks in advance !!!


===================================================
Eduardo Andrés León
Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 5054)
e-mail: eandres at cnio.es        Fax: (+34) 91 224 69 76
Unidad de Bioinformática       Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas
C.P.: 28029                Zip Code: 28029
C/. Melchor Fernández Almagro, 3    Madrid (Spain)
http://bioinfo.cnio.es	http://bioinfo.cnio.es/people/eandres
===================================================