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.

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.



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