HOPPSIGEN contains many annotations associated to retroelements and to their functional homologous genes. If you want to browse the database efficiently, you need to use keywords, types and other features.

Different kinds of annotations are available to be used in WWW-Query (use the names written in bold characters):

Type
- ppgene: type associated to retroelements
- CDE: type associated to retroelement regions similar to CDS
- 5'FL: type associated to retroelement regions similar to 5'UTR (5' untranslated region).
- 3'FL: type associated to retroelement regions similar to 3'UTR (3' untranslated region).
- repeat_region: type associated to repeat sequences.
- polya_region: type associated to polyadenylation track.
- direct_repeat: type associated to direct repeat sequences flanking retroelements.

Keywords
- i<x%: where x is a number between 0 and 100, this keyword returns all sequences (processed pseudogenes) showing a similarity less than x%. This keyword is associated to CDE regions and ppgene regions.
- CG<y%: where y is a number between 0 and 100, this keyword returns all sequences showing a G+C composition less than y%. This keyword is associated to CDE regions, ppgene regions and CDS
- chromosome name: this keyword is associated to processed pseudogenes chromosome location. Just enter the name of the chromosome as this HSn for human and MMn for mouse (n is the chromosome number) to get all processed pseudogenes located on this chromosome.
- putative_orf: this keyword is associated to sequences having a conserved open reading frame (ORF).
- putative_retroelement: this keyword is associated to sequences for which we lack evidence to class them as retroelements whithout no doubt.
- 5FL_truncated: this keyword is associated to 5' truncated retroelements.
- 3FL_truncated: this keyword is associated to 3' truncated retroelements.
- Swiss-Prot-TrEMBL accession number: this keyword is associated to retroelements homologous to a swissprot-trembl protein. Just enter the accession number of a protein to get its homologous retroelements.
- ENSEMBL geneid: this keyword is associated to retroelements homologous to an ENSEMBL gene. Just enter the ENSEMBL gene name to get its homologous retroelements.
- gene name: enter a gene name enclosed between stars to get all retroelements related to this gene.

Species or taxons
- homo sapiens or homo: to select human sequences.
- mus musculus or mus: to select mouse sequences.

Some useful examples of request are available here.

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