HOPPSIGEN can be used for different queries. We made a list of examples of few useful queries made with WWW-Query.
The order of each query is important. For example, to make a query only on CDE regions, the type CDE must be used before the main query.
1) How to extract all human processed pseudogenes located on the X chromosome, showing a similarity less than 90% with their functionnal paralogous genes and having a GC content less than 50%?
Chromosome location for human genome is described by the keyword HSn. Similarity between the processed pseudogenes and its functional paralog is defined by the keyword i<90%. GC content of the processed pseudogene is described by the keyword CG<50%. In order to select only processed pseudogenes, the type ppgene must be added at the end of the query.
2) How to extract all processed pseudogenes homologous to an SPTREMBL gene?
For example, we are looking for all processed pseudogenes homologous to the SPTREMBL protein Q9NV69. The best way to do this is to make a Search for families, alignments and trees containing this keyword.
3) How to extract all human CDEs (coding exons) showing a high similarity level with their functional paralogs?
The similarity level for CDE is defined only on regions similar to the CDS of the functional paralogous gene. In order to make this request, the best way is to select a Search for sequences. First, the species must be defined: homo in our example. The type CDE must be selected. Then, the keyword i<95% should be selected with the option AND NOT in the left menu to exclude all CDE having a smilarity level smaller than 95%. The same request should be done for mouse by replacing "homo" by "mus" in the field "species or taxon".
4) How to extract all mouse processed pseudogenes (ppgene) not truncated either in 5' nor in 3'?
The best way is to make a Search for sequences. First the species mus must be selected. Then, the type ppgene must be chosen to select only processed pseudogenes. Then, you should use the the keywords 5FL_truncated and 3FL_truncated and select AND NOT in the left menu to remove all processed pseudogenes truncated in their 5' regions and/or their 3' regions.
5) How to extract all families related to cytochrome genes ?
First, you need to select Search for families, alignments and trees to make q query on families. Then, the keyword cyotchrome should be used enclosed between stars like this: *cytochrom*.
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