ABC: software for interactive browsing of genomic multiple sequence alignment data

doi:10.1186/1471-2105-5-192

BMC Bioinformatics

Volume 5

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Software

ABC: software for interactive browsing of genomic multiple sequence alignment data

Gregory M Cooper¹ , Senthil AG Singaravelu¹ and Arend Sidow¹^,2

¹Department of Genetics, Stanford University, Stanford, CA 94305-9010, USA

²Department of Pathology, Stanford University, Stanford, CA 94305-5324, USA

author email corresponding author email

BMC Bioinformatics 2004, 5:192doi:10.1186/1471-2105-5-192


Published:	8 December 2004

Abstract

Background

Alignment and comparison of related genome sequences is a powerful method to identify regions likely to contain functional elements. Such analyses are data intensive, requiring the inclusion of genomic multiple sequence alignments, sequence annotations, and scores describing regional attributes of columns in the alignment. Visualization and browsing of results can be difficult, and there are currently limited software options for performing this task.

Results

The Application for Browsing Constraints (ABC) is interactive Java software for intuitive and efficient exploration of multiple sequence alignments and data typically associated with alignments. It is used to move quickly from a summary view of the entire alignment via arbitrary levels of resolution to individual alignment columns. It allows for the simultaneous display of quantitative data, (e.g., sequence similarity or evolutionary rates) and annotation data (e.g. the locations of genes, repeats, and constrained elements). It can be used to facilitate basic comparative sequence tasks, such as export of data in plain-text formats, visualization of phylogenetic trees, and generation of alignment summary graphics.

Conclusions

The ABC is a lightweight, stand-alone, and flexible graphical user interface for browsing genomic multiple sequence alignments of specific loci, up to hundreds of kilobases or a few megabases in length. It is coded in Java for cross-platform use and the program and source code are freely available under the General Public License. Documentation and a sample data set are also available http://mendel.stanford.edu/sidowlab/downloads.html webcite.