In this article we present the first version of Gypsy Database PROfessional (GPRO 1.0) a software for annotation, data processing, management and analysis of DNA/RNA and protein databases (including host genes, repeats and mobile genetic elements).

In this article we introduce the release of TIME (Tool for In-place Mo-lecular Editing), a sequence editor devoted to the analysis of large nucleotide and protein sequences such as chromosomes, genomic contigs and their encoded protein products.

In this paper we introduce version 2.0 of CheckAlign, an open source application oriented to bioinformatic analyses based on information theory and the Shannon-Weaver algorithm.

The GyDB (Gypsy Database) collection is a non-redundant repository of multiple alignments, hidden Markov model profiles, and majority-rule consensus sequences. The collection is based on all currently known protein domains of the distinct mobile genetic elements and related host genes classified at "Gypsy Database of mobile genetic elements". Alignments are available in six formats: FASTA, PIR, MSF, Stockholm, Clustal and Phylip. Hidden Markov model profiles and consensus sequences are constructed based on each protein domain consensus accepted per monophyletic group of classified MGEs and protein domains. The GyDB collection was originally launched as a resource of Biotechvana Bioinformatics that is related to, but it is independent from, the Gypsy Database. This relationship has recently motivated us to finally deposit the GyDB collection within the Gypsy database, where the resource is now publicly accessible as a permanent section.

In this paper, we present the second release of the GyDB Collection: an in-progress repository of manually refined multiple alignments, Hidden Markov Model (HMM) profiles and Majority-rule consensus (MRC) sequences of viruses and mobile genetic elements. Alignments are available in multiple formats plus a color-shaded HTML for preserved motif visualization. The HTML format includes links to each sequence?s GenBank accession at NCBI. HMM profiles and MRCs are based on each of the accepted protein domain consensus accepted per monophyletic group of mobile genetic elements (MGEs) and protein domain. The collection is the repository of the Gypsy Database (GyDB) of Mobile Genetic Elements and contemplates all protein domains encoded by all phylogenetic subsets of MGEs classified at GyDB and, as such, is subjected to continuous growth.

RMXSC is a PHP server for converting Reference Manager's exported databases from XML format to a SQL format suitable for most common database engines. The server filters non useful information and avoids repeated entries. The PHP script may also be downloaded under open source license for installation and personalization in other servers and computers.

Biotechvana Queue Manager is a server overload preventing script for PHP-based Web sites. This script manages all requests received in a web server to a target application. The tool registers them in a queue controlled by a database engine and processes each request sequentially, one at a time. It operates transparently, telling the user how much time remains for a request to be performed.