Each binary file contain a coordinate offset and thus any desired location in chromosome is rapidly accessed by moving the file pointer across the binary file with respect to this coordinate offset.
After the data were aligned, sequence postprocessing tool (SAMtools) was used to store, sort, and index the binary SAM data (bam files) with respect to sequence alignment (http://samtools.sourceforge.net) [ 22].
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Eight gene trees conflicted with the consensus tree (Additional File 1) with respect to relationships among the four grasses examined.
In order to identify consensus reactions we grouped all calculated flux profiles into 13 sets (LS24, LS40, LS50, eRing, lRing, eTropho, lTropho, eSchiz, lSchiz, Mero, Gameto, ooSporo, sgSporo; see Additional file 3) with respect to represented stages and determined those reactions that carry a non-zero flux in all flux profiles of the same set.
The numbers and percentage of ITS-VTs for each genus are shown in Additional file 2. With respect to genera, Glomus was dominant, i.e., Glomus was represented by the largest proportion of ITS-VTs for continent, biogeographical realm, climatic zone and supercontinent, totally accounting for 74%.
Statistics of the gene signatures are further summarized in Table S2 (Additional File 1) with respect to ten functional categories: (1) tumor versus non-tumorous liver comparison, (2) survival/recurrence, (3) cirrhosis/dysplasia, (4) etiology, (5) differentiation, (6) invasion/metastasis, (7) genomic alterations, (8) modulation by a gene/protein factor, (9) HCC subgroups, and (10) other nature.
The raw SCF chromatogram files were clipped with respect to quality, repeats, and vector content.
The task is defined as ' task (out <− in)', meaning that it is executed only if ' out' file needs to be updated with respect to ' in' file: for example, if ' output.file' file does not exist, has zero length, is an empty directory or has been modified before ' input.file'.
