We store data in a customized file format without relying on a relational database, which facilitated our design of linear-time integration algorithms that can efficiently identify overlapping genomic regions in different data files.
As input, Tangram uses reads aligned to the genome reference sequence as well as to ME reference sequences obtained from RepBase [ 47], available in a customized BAM format alignment file(s) that contains MEI detection information within an optional field, the ZA tag, to indicate that a read's mate (in the case of fragment-end read pairs) maps to one of the ME reference sequences.
There is no inherent advantage in customized formatting of references, for example, whether cited as F. R. Smith, P. Y. Young and G. T. Jones J. Interest.
A total of 84 unique identifiers were used for the development of a customized 384-well format gene array panel (Table 1).
The data exchange format is a customized XML schema, which is downloadable as an additional file of this manuscript (Additional file 1).
As we were interested in a comprehensive examination of DNA methylation changes in a medium-throughput format, we developed a customized CHO CGI microarray to simultaneously analyze multiple samples of enriched methylated DNA and detect differentially methylated genomic regions.
We used the Illumina Golden-Gate assay for large-scale SNP validation, utilizing a customized design based on the 384-format Genotyping Assay.
We believe gff2sequence may represent a valuable and easy to use alternative for the generation of a customized sequence dataset from general feature formatted file.
* Custom Region: Capture a customized rectangular shape on your desktop.
The ontological hierarchy can be visualized via a customized interface that exports data to a Newick format tree, which can be subsequently observed in Figtree [41] or other Newick tree visualizers (Fig. 5).
Our current metadata text file header system also does not make use of the extensive and verbose BIR-TAB format, and would likely require a customized storage solution in YeastMine.
