The obtained sequences were assembled into contigs using the SecMan Pro module of DNAStar Lasergene sequence analysis software suite (DNASTAR Inc., Madison, WI).
In an attempt to simplify this process, we have built many of these tasks into the core functionality of the evolving Utopia protein sequence analysis software suite (30, 31).
The raw sequence data were assembled and analyzed using DNA sequence analysis software (Lasergene software suite V6.0, DNASTAR).
We assembled all sequences using the STADEN software suite (Staden 1996).
We analyzed the mappability of mouse rDNA using BEADS (Cheung et al. 2011), a bias-correction software suite for sequencing data.
Sequence analysis, BLAST searches, and prediction of ORFs were carried out using the SeqMan and EditSeq programs, and PCR primers were designed using the PrimerSelect program in DNASTAR Lasergene 8 (software suite for sequence analysis, version 8.0.2(13) 412).
Here, we present an approach to evaluate the confidence levels of TFBSs using the tools, 'matrix-quality' (86, 87), 'peak-motifs' (88), 'footprint-discovery' (89) and 'matrix-scan' (90), that belong to the software suite regulatory sequence analysis tools (90).
Motivation: RUbioSeq has been developed to facilitate the primary and secondary analysis of re-sequencing projects by providing an integrated software suite of parallelized pipelines to detect exome variants (single-nucleotide variants and copy number variations) and to perform bisulfite-seq analyses automatically.
Sequences were assembled using the PHRED/PHRAP/CONSED software suite [ 71].
Sequence analysis was performed using the computer software suite Lasergene (DNAstar, WI).
Sequence analysis was performed using the Emboss software suite [ 37], Clustal W [ 38] and 3DCoffee [ 39].
