Biotechvana Bioinformatics (BiBi)

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


Prototipo de servidor web para el análisis bioinformático de datos de citometría de flujo
Gómez-González, A., Zamora I., Soriano, B., Llorens, C.
In this article we present the prototype of a bioinformatics server (Cytometry Biotechvana) for flow cytometry data analysis. The aim of this prototype is to evaluate the requirements and needs of workflows and pipelines for analysis of this type of data.

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).

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.

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.

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.

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.

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