PRABI
Rhone-Alpes Bioinformatics Center


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PBIL Tutorial

Cross Taxa Tutorial

How query databases according to complex taxonomic critera

Cross-Taxa allows to retrieve gene families that are shared by a given set of taxa, or which are specific to a set of taxa. It is also possible to select genes families which are associated to a certain set of taxa but which are not found in a second set of taxa. Any taxonomic level can be used.

Cross-Taxa gives access to a family retrieval system based on taxonomic criteria. Its web interface is composed of two text fields. It allows to retrieve all gene families that are shared, strictly or not, by a first set of taxa defined in the first field (list1) and that are not associated with a second set of taxa defined in the second field (list2). Any taxonomic level can be used and mixed to compose the query (e.g., Homo sapiens, Primates, Mammalia ). For example it is possible to retrieve the families of bacterial genes specific to a toxic strain of Escherichia coli, or to retrieve the gene families found in mammals but not in birds or as well to retrieve gene families which are found in mammals only.

The first set of taxa can be used for an inclusive or exclusive selection of families.

It is as well possible to pre-select the families by the number of sequences/species. For example it is useful to avoid families presenting only one sequence or one species.


Two types of search are available, "Inclusive Search" and "Exclusive Search" :

 Inclusive Search :

Any family containing at least one species from each taxon of the list will be selected

Example 1.1 : Hovergen families with Primates and Rodentia sequences

If you specify Primates and Rodentia in the list1 (with an empty list2) you will get all the families with at least one sequence from Primates and one sequence from Rodentia .


Example 1.2 : Hovergen families with sequences from Human and Mouse

if you specify Homo and Mus in the list1 (with an empty list2) you will get all the families with at least one sequence of Homo and one sequence of Mus ( for example a 3 sequences-family, with one sequence from Homo sapiens, one sequence from Mus musculus and one sequence from Bos bovis).


Example 1.3 : Hovergen families with mammalian sequences but not primate sequences

If you specify Mammalia in the list 1 and Primates in the list 2, you will get all the families with at least one sequence of Mammalia but no sequence from Primates ( for example a 15 sequences-family, with 5 sequences from Bos bovis, 5 sequences from Mus musculus, 2 sequences from Rattus norvegicus and 3 sequences from Xenopus).


 Exclusive Search :

Any family containing only species from all the taxa of the list (i.e. none from other taxa) will be selected

Example 2.1 : Hovergen families with primates sequences only

If you specify Primates in the list1 (with an empty list2) you will get all the families with sequences from Primates only. Note that the families with at least 2 sequences have been selected, to avoid the monosequence families.


Example 2.2 : Hovergen families with sequences from Human and Mouse only

If you specify Homo and Mus in the list1 (with an empty list2) you will get all the families with at least one sequence of Homo and one sequence of Mus and no sequence from any other species ( for example a 3 sequences-family, with 2 sequences from Homo sapiens and one sequence from Mus musculus).


Example 2.3 : Hovergen families with primates sequences only and with at least one human sequence

If you specify Homo and Primates in the list1 (with an empty list2) you will get all the families with sequences from Primates only and at least one sequence from Homo ( for example a 5 sequences-family, with 3 sequences from Homo sapiens and 2 sequences from Pan troglodytes).Note that the families with at least 2 sequences have been selected, to avoid the monosequence families.


Example 2.4 : Hovergen families with mamalian sequences only but not primate sequence

If you specify Mammalia in the list 1 and Primates in the list 2, you will get all the families with at least one sequence of Mammalia and Mammalia only and no sequence from Primates ( for example a 18 sequences-family, with 3 sequences from Bos bovis, 7 sequences from Mus musculus and 8 sequences from Rattus norvegicus).Note that the families with at least 2 sequences from 2 different taxons have been selected.


More on Search Families by Cross Taxa ...
Cross-Taxa queries may take time. For very simple queries on families (for example, to retrieve all the families containing a sequence of mammalia), we recomand to use WWW-Query.