Patterns may be aligned to existing alignment marks without exposing the writing area by using the alignment program AL.
In addition, we built a phylogenetic tree (Fig. S1) of all of the clones listed in Table 1 and Table S2, clearly showing the phylogenetic context of the respective clades and the monophyletic nature of each TRF (a maximum likelihood tree was built using RaxML [38] from sequences aligned to the SILVA 16S database [39] using the SINA alignment utility.
In release 5.0, all transposon-related sequences were uniformly classified by searching the entire genome against a curated database of protein-coding transposon sequences [ 80] using the dps alignment utility of the AAT package and automatically applying the corresponding transposon family annotation.
In order to ensure consistent representation of INDELs, both SOLiD and Illumina BAM files were realigned at runtime using the left alignment utility in the FreeBayes variant caller package (bamleftalign), and were split in cases where mismatches could be resolved by a larger insertion or deletion using gap-opening realignment (ogap) [ 11].
The FL-cDNAs that were not fully integrated into gene structure annotations include aberrantly spliced transcripts, antisense mRNAs, polycistronic mRNAs, mRNAs encoding short, partial or unidentifiable ORFs, mRNAs with non-consensus splice sites, and mRNAs that did not align well to the genome using the spliced alignment utilities employed.
Then, the protein alignment was transformed into a coding sequence alignment using the "Bio::Align::Utilities" module of the BioPerl package (http://www.bioperl.org/, last accessed February 6 , 2013.
Then, the protein sequence alignment was converted to a coding sequence alignment using the "Bio::Align::Utilities" module in the BioPerl package (http://www.bioperl.org/).
We then used the alignment data to map the human miRNA genes to the rhesus and mouse genomes with the LiftOver utility [42] to obtain the genome coordinates of potential miRNA genes in the two genomes.
We realigned all reads within candidate SV sites using Smith Waterman-based alignment utilities provided through the Biostrings package (Pages et al., 2013) in Bioconductor (Gentleman et al., 2004), with parameters reflecting the probabilities of observing alignment errors, explained further in Section 2.4 and Supplementary Material 'Smith Waterman alignment parameters' (Malde, 2008).
Verification of alignments was performed using the BLAST2Sequence utility at NCBI [ 19].
