While both these regions contained small indel events and multiple nucleotide degenerate sites, resulting in multiple plausible evolutionary histories, the posterior alignment distribution from BigFoot exhibited how our joint model reliably aligned all instances of the binding site together.
Based on this result we constructed a specific Hidden Markov Model by aligning all the identified thioredoxin-like domains, and using this to screen the remaining SEO proteins for similar domains.
The expectations were: 1) to obtain an exhaustive collection of genes selectively over-expressed in late schizont stages; 2) to validate or invalidate P. falciparum gene models by aligning all ESTs with the genome sequence, and 3) to identify genes indicating protein polymorphism between the FcB1 and 3D7 strains.
The cmalign program takes a CM file (calibrated or not), aligns all sequences to the model and outputs a structurally annotated MSA in Stockholm format.
Aligning all pairs of neighbours aligns all ions.
Parent-derived models were constructed by aligning all fully-supported gene models (i.e., gene models with full-length cDNA transcript support) to the genomic sequence of GPFs.
DAMSUP was used to align all models with the most probable one, and all of the aligned models were averaged in DAMAVER to compute a probability map.
Inspired by the approaches of Strecha et al. [35] and Untzelmann et al. [36], we aligned all models to the OpenStreetMap [37].
However, in our case, the model was not able to align all patients according to one trajectory but rather identified statistically two populations, based on fast or slow progression in the CDR-SOB score.
Multiple alignment was created by aligning all sequences against Hidden Markov Model GTP_EFTU from Pfam [ 105] using program HMMALIGN [ 18].
