Help

From The Gypsy Database

In this Help are briefly described the GyDB sections shown on the top and side menus. Please, note that some sections are only available to registered users.

Contents

Top menu

Main

The main page of the Gypsy Database. It also contains a link to the Editor's Guide, a page that describes in details how users can edit and format the contents of the GyDB using the wiki language.

BLAST

A BLAST search server powered by the NCBI BLAST package which allows users to compare both nucleotide and protein queries with the non-redundant sequences collected into the GENOMES, LTRs and CORES databases (also available for download on the side menu). It permits to select different search programs as well as filtering among the different protein domains.

HMM

HMM server allows users to compare protein query with the GyDB database of Hidden Markov Model (HMM) protein profiles. Moreover it permits comparisons between HMM profiles and sequences in the CORES database. In this server is also possible to obtain the complete list of HMM profiles available on GyDB.

Literature

Our literature server database which contains more than 100.000 non-redundant citations in the topic. Search by different criteria referred to the Journal (name, year and volume), to the authors or to the title. Each citation links to the PubMed Central digital archive at NCBI.

Data submission

Users can submit their own data regarding database topics (adding to the GyDB new superfamilies, families, domains and related families), phylogenies (with links to element templates), nucleotide or protein sequences for BLAST server, HMM profiles, majority-rule consensus sequences (MRC) and literature references to contribute to improve the contents of the Gypsy database.

This section is only accessible for registered users.

Subscribe

This section is for authors who want to register to the Wiki, contributing with their knowledge or editing contents to improve and expand GyDB topics. For registration, authors should agree the terms of use.

Contact

Contact with the GyDB Technical Support and the Editors-in chief.

Search

There are two search options: search any term through all contents of GyDB or, alternatively, search mobile genetic elements only by introducting the element’s acronym to be automatically directed to the corresponding element's datasheet.

GyDB people

Join the GyDB scientific social network, a private space where subscribers can create personal profiles for sharing personal and academic information, topics of interest and communicate with other network members through a private messaging system. The network also provides additional tools such as personal blogs, a wall and personal photo galleries.

This section is only available for registered users.

Login

At the top right is located the link to the “log-in” option for the registered user access.

Side menu

Main

This section contains an introduction to the project of analyzing and classifying the non-redundant diversity of mobile genetic elements (MGEs).

Superfamilies

This section shows the classification of Retroelements (retrotransposons and retroviruses) that currently are divided into four systems or groups: long terminal repeat (LTR) retroelements, the non-LTR retroelements, the tyrosine recombinase (YR) retroelements and the Penelope retrotransposons. Each group is presented with a short description and a graphic representation of its genomic structure. The highlighted bibliographic citations -filed in the Literature database- link to the corresponding NCBI-PubMed archive.

Systems

Here is reported the LTR retroelements system, one of the four major groups of retro-transcribing mobile genetic elements. It includes LTR retrotransposons (Ty3/Gypsy, Ty1/Copia, Bel/Pao families) and retrovirus, and other non-autonomous retroelements evolved from LTR retroelements (LARDs and TRIMs). In this system has been also considered Caulimoviruses because of their common evolutionary relationship with the autonomous LTR retroelements. Each category is presented with a short description and a graphic representation of its genomic structure.

Families

This section encompasses all LTR retroelement families (Ty3/Gypsy; Ty1/Copia; Bel/Pao and Retroviridae) and plant caulimoviruses (Caulimoviridae family) currently investigated in the GyDB. All families link to its own section that provides an exhaustive and updated discussion, graphic representations of the genomic structure and several bibliographic references of interest.

Classified elements

The complete list of the elements currently classified in the database including a short discussion, taxonomy information, genomic structure, and several bibliographic citations, as well as a link to the related NCBI GenBank accession. Classified elements can also be accessed through the specific search option at the top menu.

Related families

The section includes two categories of protein products (Chromodomain superfamily and the Clan AA of aspartic peptidases) commonly encoded by LTR retroelements and their host genomes including a description of their structural and functional characteristics and including graphic representations.

Domains

This section collects the domains typically observed in the genomic structure of the different elements classified in GyDB.

Trees and networks

A collection of inferred phylogenetic trees based on the distinct single protein domains encoded by the classified elements, or based on their concatenation (when they are part of polyproteins), including links for each retroelement to its description template or to the sequence's GenBank accession at the NCBI when not available. This section also includes the Clan AA (Aspartic peptidases) Reference Database (CAARD) ancestral reconstruction based on 323 non-redundant sequences belonging to different clan AA families (proteolytic enzymes).

RefSeq databases

This section contains the three databases (GENOMES, CORES and LTRs) implemented in the BLAST server. The databases collect respectively the full-length genomes, the protein sequences and the LTR sequences corresponding to all elements investigated in GyDB. Clicking on each database the users can download the related zipped file.

Links of interest

A collection of links of interest.

Former versions

A link to the Gypsy Database v1 former version.

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