With a Perl program using a pattern match representing the 4,096 possibilities and NCBI BLAST standalone tool the sequences were scanned for possible HMGA2 binding sequences.
miRSeq is a user-friendly standalone toolkit for sequencing quality evaluation and miRNA profiling from NGS data.
Hydrophobicity values of proteins were retrieved from ProtParam [ 73] Residue-wise burial in proteins was computed by a standalone version of sequence-based prediction program RVP-Net [ 74].
In order to remove potentially contaminated sequences, standalone blast (blastn) was used to match reads against the pDNR-lib vector (Clontech, Mountainview, CA, USA) used in the cDNA library construction.
On the other hand, in " miRSeq: a user-friendly standalone toolkit for sequencing quality evaluation and miRNA profiling," C.-T. Pan et al. introduced a new tool for NGS data alignment that not only is easy to implement but also offers various methods for evaluating sequencing quality and provides profiles for up to 105 species for users to compare with.
Genome searches were conducted using standalone BLAT (v35) fast sequence search command line tool [ 74] and GeneWise (v2.2.0) was used as a homology based predictor of gene structure [ 75] with chicken and green anole α-keratin sequences downloaded via NCBI (Additional file 6).
In addition, it also contains several standalone tools for performing protein sequence digestion, creating spectrum and sequence decoy databases [43], and performing open modification spectrum library searches (QuickMod/Liberator) [44].
Over the past few years, several web-servers and standalone applications, analyzing deep sequencing data for miRNA discovery and/or expression profiling, have been reported; the web-servers include miRCat [ 6], miRAnalyzer [ 7], miRTools [ 8], whereas the standalone tools include miRDeep [ 9], miRExpress [ 10], MiroPipeline [ 11], etc.
Sequence homology searches were performed using the standalone BLAST suite against D. melanogaster sequence databases (release 5.4) available in the FlyBase repository [ 66].
Meanwhile, "Dracula Untold," the 2014 fantasy starring Luke Evans, was originally intended to kick off the Dark Universe, but Universal has since sidelined that film as a standalone, opting to launch the sequence with "The Mummy" instead.
