To avoid HOEs, PSI-Search always uses the alignment boundary information from the first significant alignment in which a library sequence appears.
Finally, structural and functional annotations (including known domains from the Interpro database: www.ebi.ac.uk/interpro/) were added using the multiple alignment information management system (MACSIMS) [58].
The Illumina mate pair reads were filtered out using the contig alignment information.
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.
To achieve this, we process the set of blocks as follows: for each block, the alignment information is used to calculate a bidirectional mapping between the coordinate system of the SuperGenome and the original coordinates of each input genome contained in the block.
Instead, the consensus is recalculated using read alignment information, and when multiple bases occur at the same frequency, the alphabetically smallest one is chosen to be the consensus.
Orthology assignments were determined using multiz alignment information [ 19], the "chains and nets" data from the UCSC Human Genome Browser mysql tables [ 20].
Then we recompute the consensus using alignment information alone to further avoid the misrepresentation of the consensus during variant calling.
The nucleotide sequence was then aligned using the amino acid alignment information, using a scripted pipeline.
Nevertheless, in order to make the tests as challenging as possible, we introduced read errors as described above, applied HMMER instead of using true alignment information, and conducted analyses after deleting the true target species from the tree in all subsequent analyses reported below.
