Two formats are available: the original e-mail format, and a paginated indexed format suitable for printing on a line or page printer.
[ 19] Essentially, grey literature includes documents that have not been formally published in a peer-reviewed indexed format.
While it may take a few minutes to convert the input text file to the indexed format, once this is done there is no need to upload the entire file, and the response time on the browser is nearly as fast as if the file resided on the local UCSC server.
Thus, indexed formats can efficiently support views only for a limited range of resolution scales.
Indexed formats include articles, books, chapters of edited books, dissertations, and other publications.
Indexed formats include BAM and Goby [ 14 ] for sequence alignments.
Indexed formats provide rapid and efficient access to subsets of the data for display, but only when zoomed in to a sufficiently small genomic region.
This data can be made available in simple flat file formats (e.g. FASTA) or various indexed formats (Bowtie [ 7], BWA [ 8], Blast [ 9]), depending on the requirements of each tool.
This would include collection and storage of descriptions of the samples, reagents, technology platforms, protocols and analysis methods in an indexed, standardized, structured format.
In the same line, genomic annotation and intervals are often made available in BigBed format, an indexed binary version of BED.
BigWig files are a compressed, indexed, binary format for genome-wide signal data for calculations (e.g. GC percent) or experiments (e.g. ChIP-seq/RNA-seq read depth).
