Table 2

A comparison of the Visualization Capabilities and Data Integration of the different tools currently available with those of GenomeGems
Tool View Data integration
ABC [14] Three distinct display modes: NA
1. A very low resolution- histogram
2. Intermediate resolutions- a ‘Wiggly Plot’
3. Very high resolution - the user may view the sequence data directly.
EagleView [15] Compact with zooming capability. Genome features (exon, intron, etc.), Polymorphism data (e.g. SNP), 454 flowgram trace, Illumina four color raw signals.
Pinpoint view of: base quality, technology-specific sequence trace, read ID and strand.
LookSeq [16] 1. A resolution from the level of a whole chromosome to the level of individual bases. LookSeq can visualize read alignments and some basic properties as separate “tracks”:
2. There are options to view genome coverage, GC content, and annotations to the reference sequence. 1. Sequence annotation
2. Coverage
3. GC contents
This information is taken from the alignment databases as well as some auxiliary files.
Magic Viewer [17] The short read image can be zoomed to any resolution, from a whole chromosome to individual bases at any desired level. NA
Also displays auxiliary information: read ID, location, base quality, read length and orientation.
Tablet [18] The main display provides a view of a single contig at a time, with reads aligned against their consensus sequence. NA
GenomeGems Five separate analysis methods are available: GenomeGems integrates well with the UCSC Genome Browser, for the purpose of visualization of SNPs, in addition to the analysis and visualization in the actual tool.
1. Data Table - displays the data supplied by the user and analyzes the percentage of mutant reads, in spreadsheet format, enabling analysis within the tool in addition to fast export to Excel. UCSC custom tracks supply additional data calculated by UCSC such as: context of the SNP – CDS or intron, and the properties of the changed amino acid – polarity, acidity and hydropathy.
2. Sample Comparison - displays a bar graph presenting the frequency of each SNP in the investigated samples, according to a threshold value.
3. SNP-View - displays a table containing the numbers of samples that include each SNP in a specific chromosome.
4. Translation of the input file into a PgSNP file format for a later visualization in the UCSC, as a UCSC Custom Track.
5. Additional Information- suggests additional external links for further investigation and annotation of specific SNPs and of the impact of amino acid changes on human proteins.

Abbreviations: NA, Not available; PgSNP, Personal Genome SNP; CDS, Coding Sequence; UCSC, University of California Santa Cruz.

Ben-Zvi et al.

Ben-Zvi et al. BMC Research Notes 2012 5:338   doi:10.1186/1756-0500-5-338

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