New Jersey's 1981 law allowing judges to extend penalties for crimes committed because of a defendant's prejudices is unconstitutional, the United States Supreme Court ruled last week.
To perform multiple-sequence alignment, gap open and extend penalties were set to 10 and 0.2, respectively.
To account for the high-coding density in bacterial genomes, we performed ungapped searches (gap open and extend penalties 1000).
We used BLAST (Altschul et al., 1990) to identify the location of reads that could be aligned unambiguously to one location on the genome, with default BLAST parameters, except for gap open and extend penalties, which were set to 1.
Current sequence alignment methods typically score pairwise alignments with an affine gap scoring scheme consisting of a gap open penalty and a gap extend penalty.
The parameters used were: gap opening penalty: 10; and gap extend penalty: 0.1.
Targets for Senegalese sole miRNAs were predicted using the following default parameters: Gap open penalty, -9.0; gap extend penalty, -4.0; score threshold, 140.0; energy threshold, 1.0 kcal · mol-1; scaling parameter, 4.0.
To test the data for a possible presence of long common motifs over-represented in the sequences of eRNAs, Clustal algorithm [ 27] was used with gap open and gap extend penalty parameters varying from 1 to 10.
Database searches using the BLAST were performed using the Tera-BLAST™P algorithm, open penalty 11, extend penalty 1, double-affine Smith-Waterman window 50, and maximum e-value cutoff 1 × 10-3 on TimeLogic DeCypher hardware (Active Motif, Inc., Carlsbad, CA).
MiRNA target sites in the 3'-UTR of murine mRNAs Srebf2, Hgmcr, Hgmcs1, Mvk, Idi1, Fdft1, Cyp51, Sc4mol, and Ldlr were predicted using miRanda (version 3.0; [ 36]) with the following parameter settings: minimum score 130, minimum free energy −19 kcal/mol, conservation off, scaling parameter 4, gap open penalty −8.0, gap extend penalty −4.0.
Alignments of intron sequences of SlAP3X and SlAP3Y were conducted using the Needle program within the EMBOSS 6.5 package (Rice et al. 2000) with default settings, except that the gap penalty was set to 30.0 and the extend penalty was set to 0.0.
