Here, the Baker laboratory's in-house alignment program, K sync, produces a group of sequence homologs, and each of these is modeled by the Rosetta de novo method to produce a decoy (possible structure).
The reference structure alignments for the training and validation data are built using our in-house structure alignment tool DeepAlign.
For all benchmarks, we use four structure alignment tools to generate reference alignments: TM-align (Zhang and Skolnick, 2005), Matt (Menke et al., 2008), Dali (Holm and Sander, 1993) and our in-house structure alignment tool DeepAlign.
In this study, we have developed three different work flows dedicated to ISs and MITEs detection: the first two use de novo methods detecting either repeated sequences or presence of Inverted Repeats; the third one use 28 in-house transposase alignment profiles with HMM search methods.
Using our in-house tools, sequence alignment for each contig can be displayed in either bird's-eye view or nucleotide-level resolution, facilitating close examination of assembly quality, genetic polymorphisms, sequence repeats, and sequencing errors.
We also carried out similar syntenic analysis using either in-house constructed global alignments with BLASTZ [ 42] or cross-species liftOver data from the UCSC browser and obtained similar result, and thus was not discussed here.
Sequences retrieved from Blast searches were automatically integrated into the corresponding alignments and aligned using CLUSTALW, implemented in our in-house automated Blast and alignment pipeline.
To conserve the frame of the coding sequences, the nucleotide alignment is derived from the amino acid alignment (in-house script) of the translated products of the pseudogene and its cognate gene obtained by GENEWISE.
Finally, all FASTA strings were translated into rCRS-coded haplotypes using SAM [25] and subsequently checked with in-house software to harmonize alignment.
Using in-house perl scripts, the alignment information was further parsed to generate forward and reverse mapping information at each site, resulting in a configuration of eight numbers for each line (A, a, C, c, G, g, T, t), corresponding to the number of reads mapped at each genomic position in the reference sequence.
Coverage data are summarized in Supplementary Tables 1 and 2. In-house bioinformatic analysis included alignment to UCSC hg19, using Burrows-Wheeler Aligner; duplicate removal (Picard v1.85) and variant detection (Varscan v2.2) (Koboldt et al., 2009), Dindel v1.01 (Albers et al., 2011).
