During preprocessing, all chromosomes are processed in parallel; in the clustering stage, chromosomal segment pairs are processed in parallel with the space distributed evenly between processors.
In the present work, each chromosome was processed independently and data were analyzed by using the PLS procedure of SAS® software (SAS® institute Inc., Cary, NC).
Previous reports (Chang et al, 2008; Wang et al, 2008) indicated that mature miR-29 family members encoded on the same chromosome are processed from a common primary transcript (pri-miRNA, Figure 3C).
Chromosome images were processed using the ScionImage and Adobe Photoshop v. 6 software.
The brains of three adult heterozygous ALDH1L1 – eGFP-L10a bacterial artificial chromosome (BAC) transgenic mice were processed for immunocytochemistry using antibodies against enhanced green fluorescent protein (eGFP), an astrocytic marker (anti-GFAP), an oligodendrocytic marker (CNP), and a neuronal marker (anti-NeuN).
Cells were processed for chromosome spreads 48 hours after transfection (or 24 hours in case of SGOL1 RNAi).
Data was divided in marker sets across chromosomes to be processed using a parallel computing cluster.
All chromosomes have been processed with TRF using alignment parameters 2, 7, 7 for match, mismatch, and indels, respectively, and a minimum alignment score of 50.
Note that fragments from different queries or database sequences (e.g., chromosomes) can be processed in a single pass by our tool but are generally chained separately from each other (even without use of clustering).
When the user follows the 'View Database' link, a connection to the database is established, and a table of all chromosomes that have been processed is shown, see Table 1.
