Biotechvana Bioinformatics (BiBi)

Journal of Biotechvana software and computational
resources in bioinformatics
ISSN 1988-7957

Summary

Software
GPRO: the professional tool for management, functional analysis and annotation of omic sequences and databases
Futami,R., Munoz-Pomer, A., Viu,J.M., Dominguez-Escriba,L., Covelli,L., Bernet,G.P., Sempere,J.M., Moya,A. and Llorens,C.
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).

Software
TIME: a sequence editor for the molecular analysis of large DNA and protein sequence samples
Munoz-Pomer,A., Futami,R., Covelli,L., Dominguez-Escriba,L., Bernet,G.P., Sempere,J.M., Moya,A. and Llorens,C.
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.

Software
CheckAlign 2.0
Munoz-Pomer,A., Futami,R., Sempere,J.M., Moya,A. and Llorens,C.
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.

Computational resources
The GyDB collection is now publicly available within the Gypsy Database of Mobile Genetic Elements
Covelli,L., Munoz-Pomer,A., Dominguez-Escriba,L., Futami,R., Bernet,G.P., Moya,A. and Llorens,C.
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.

Computational resources
The GyDB Collection of Viral and Mobile Genetic Element Models
Llorens, C., Munoz-Pomer, A., Futami, R. and Moya, A.
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.

Scripts
RMXSC server 1.0
Futami, R. Llorens, C. Vicente-Ripolles, M. and Moya, A.
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.

Database utilities
Biotechvana Queue Manager 1.0
Futami, R. Llorens, C. and Moya, A.
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.

Database utilities
Biotechvana Search Engine 1.0
Llorens, C. Futami, R. Vicente-Ripolles, M and Moya, A.
Biotechvana Search Engine is a cross-platform customizable web search engine script written in PHP that indexes in a database all the words contained in your web site or intranet to provide faster searches to your visitors. Results are sorted by relevance and a list of similar words is given when no matches are found.

Scripts
The Join Alignments Server version 1.0
Futami, R. Llorens, C. Vicente-Ripolles, M. and Moya, A.
In this work we introduce the Join Alignments Server a free accessible web-based application that allows users to automatically join several files containing multiple alignments in Fasta format into a single file. Join Alignment Server PHP-script can be downloaded in open source for installation and source code adaptation.

Scripts
The Alignment Format Converter Server 1.0
Futami, R. Llorens, C. Vicente-Ripolles, M. and Moya, A.
The Alignment Format Converter Server is a free accessible server that allows users to convert multiple alignment files from one format to one or more of the most common formats in only one step. This server is a PHP script that may be accessed online or downloaded under open source license for installation and personalization in other servers and computers.

Database utilities
GyDB Package 1.0
Futami, R. Llorens, C. Vicente-Ripolles, M. and Moya, A.
The GyDB Package is the downloadable version of our project online the Gypsy Database (GyDB) of mobile genetic elements. This package allows for deployment of a local version of the GyDB, making it possible to create your own personal database using the GyDB framework for your intranet. The package includes all the functions available on the online version of the GyDB, consisting in content and literature browsers and services, except the BLAST and HMMER programs and the images of which we are not owners. Accession to BLAST and HMM servers can be compiled and executed on local machines and the services directly link by default to the GyDB online. If you want to implement these two programs or any other tool in your own database, the package facilitates content creation and management with examples and automations.

Computational resources
The GyDB collection: Ty3/Gypsy and Retroviridae LTR retroelements and related nonviral proteins
Llorens, C., Futami, R. and Moya, A.
In this paper we introduce the GyDB collection, a non-redundant compilation of manually refined multiple alignments, hidden markov model profiles, and majority-rule consensus sequences based on all currently known protein products encoded by Ty3/Gypsy and Retroviridae LTR retroelements and related nonviral proteins. Alignments are available in six formats: Fasta, Pir, Msf, Stockholm, Clustal, Phylip plus a web-shaded HTML format to facilitate preserved motif visualization. The HTML format includes hyperlinks to each sequence?s Genbank accession at NCBI. Hidden markov model profiles and majority-rule consensus sequences were constructed based on each protein domain consensus accepted per monophyletic group of LTR retroelements and protein domain.

Software
Phylograph: A multifunction java editor for handling phylogenetic trees
Llorens, C. Futami, R. Vicente-Ripolles, M. and Moya, A.
In this work we introduce Phylograph; a multifunctional tree editor particularly indicated for large trees. The application reads trees up to 1000-1200 leaves and constructs and edits graph drawings in different layouts. Phylograph roots the tree using as outgroup a single leave or a whole branch, simply via the computer mouse. The tool incorporates a wide set of functions to expand, compress, invert, and/or rotate a tree. Phylograph allows the cutting of branches and the incorporation of decorations such as tags, brackets, boxes, and arrows. The tool also allows the user to save the tree drawing as a re-editable project and offers the choice of various exportable image formats, including a HTML format suited to databases. Phylograph is a Java application. This means that the tool runs on personal computers as a standalone program. We also present here an overview of the algorithms used by Phylograph to represent the tree drawings.

Software
The CheckAlign logo-maker application in analyses of both gapped and ungapped DNA and protein alignments
Llorens, C., Futami, R., Vicente-Ripolles, M. and Moya, A.
In this paper we introduce CheckAlign, a logo-maker application that allows users to create consensus graphical representations from the input of both gapped and ungapped alignments using information theory. The application also allows users to generate a logo using a relative-frequency algorithm to overestimate the true consensus of distantly related sequences when conventional algorithms fail. CheckAlign is available as a free online server written in PHP, and as a Java application. This means that the tool runs on most personal computers (PCs) as a standalone program.

Opinions and comments
Introducing Biotechvana Bioinformatics
Llorens, C., Futami, R., Munoz-Pomer, A., Vicente-Ripolles, M., and Moya, A.
In this paper, we introduce Biotechvana Bioinformatics; a self-sustaining initiative focusing on software advances, computational resources, and database utilities in the management of biological data. The platform facilitates access to an in-progress collection of tools presented through an online catalogue organized as an electronic journal where tool manuals and other resources are distributed by sections presented as articles.



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