The region was selected based on alignments and propensity scales.
Based on these results and the works of others, we propose an algorithm which does post-processing on alignments output by HMMs to automatically recognize vowel length.
This method generally relies on alignments of orthologous, non-coding sequences from multiple species [51].
We extracted the SNPs based on alignments between ESTs and the A. gambiae reference genome.
Degenerate primers were based on previous design considerations [63] and on alignments of previously isolated Xist genes.
The evolutionary conservation of amino acid sites with mutations was analyzed using ConSurf[25], [51], [52], based on alignments shown in Fig. S2 and S3.
All 5' targeting sites were chosen based on alignments of partially sequenced field samples (Accession numbers EU787517.1 – EU787984.1, AY462581.1 – and62851.1) and the published 3d7 var gene sequences.
To facilitate their embedding in the same genotype space, we focused only on alignments with sequences no shorter than 100 amino acids.
A number of models (100 each) were generated using Modeller 9v7 with classical approach [60] based on alignments from bSVRs and aSVRs of the target and template sequences.
Our initial inspection of these loci was based on alignments and analyses of Drosophila and vertebrate conservation available through the UCSC genome browser.
Intron indels were scored on alignments that excluded non-avian outgroups (48 taxa), UCE indels were scored on alignments that included Alligator (49 taxa), and exons were scored on alignments that included all non-avian outgroups (52 taxa).
