Dataset Information

BamBam: genome sequence analysis tools for biologists.

ABSTRACT:

Background

Massive computational power is needed to analyze the genomic data produced by next-generation sequencing, but extensive computational experience and specific knowledge of algorithms should not be necessary to run genomic analyses or interpret their results.

Findings

We present BamBam, a package of tools for genome sequence analysis. BamBam contains tools that facilitate summarizing data from BAM alignment files and identifying features such as SNPs, indels, and haplotypes represented in those alignments.

Conclusions

BamBam provides a powerful and convenient framework to analyze genome sequence data contained in BAM files.

SUBMITTER: Page JT

PROVIDER: S-EPMC4258253 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature

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Publications

BamBam: genome sequence analysis tools for biologists.

Page Justin T JT Liechty Zachary S ZS Huynh Mark D MD Udall Joshua A JA

BMC research notes 20141124

<h4>Background</h4>Massive computational power is needed to analyze the genomic data produced by next-generation sequencing, but extensive computational experience and specific knowledge of algorithms should not be necessary to run genomic analyses or interpret their results.<h4>Findings</h4>We present BamBam, a package of tools for genome sequence analysis. BamBam contains tools that facilitate summarizing data from BAM alignment files and identifying features such as SNPs, indels, and haplotyp ...[more]

PMID: 25421351

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Project description:BackgroundComparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a) provide a deep integration of sequence and structure, far beyond mapping where a sequence region falls in the structure and vice versa; (b) facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit); (c) can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc.; and (d) interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals.ResultsThe molecular graphics program UCSF Chimera includes a suite of tools for interactive analyses of sequences and structures. Structures automatically associate with sequences in imported alignments, allowing many kinds of crosstalk. A novel method is provided to superimpose structures in the absence of a pre-existing sequence alignment. The method uses both sequence and secondary structure, and can match even structures with very low sequence identity. Another tool constructs structure-based sequence alignments from superpositions of two or more proteins. Chimera is designed to be extensible, and mechanisms for incorporating user-specific data without Chimera code development are also provided.ConclusionThe tools described here apply to many problems involving comparison and analysis of protein structures and their sequences. Chimera includes complete documentation and is intended for use by a wide range of scientists, not just those in the computational disciplines. UCSF Chimera is free for non-commercial use and is available for Microsoft Windows, Apple Mac OS X, Linux, and other platforms from http://www.cgl.ucsf.edu/chimera.

Dataset Information

BamBam: genome sequence analysis tools for biologists.

Background

Findings

Conclusions

Publications

BamBam: genome sequence analysis tools for biologists.

Similar Datasets

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