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Reference alignment is obtained from the structural alignment obtained from the TMalign program [43] [i.e., TM overlap].
After threading, full atomistic models of the Rev protein were generated from the template and alignment obtained from the threading studies using the MODELLER [29], [30], and NEST software tool incorporated in JACKAL 1.5 [49].
The plant myosin sequences were added to the structure-guided multiple sequence alignment obtained from [ 23].
The observed association was significant but rather weak, possibly as a result of the genomic alignment obtained from UCSC [ 28].
We also tested the tools on a multiple sequence alignment obtained from our study on the Drosophila X chromosome.
Orthologous intron pairs were obtained through the use of a 9 vertebrate (human, chimp, mouse, rat, dog, chicken, fugu, tetraodon, zebrafish) multiple whole-genome alignment, obtained from [ 42].
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We also performed our analyses using alignments obtained from PRANK [ 42, 43], which was reported to outperform other aligners in simulation [ 46], to explore discrepancies between our results and those of Sackton et al. [ 37].
The results are based on high quality amino acid alignments obtained from a complete reannotation of the mitogenomic sequences from NCBI RefSeq database.
Multiple fCaSR exons sequence alignments obtained from PCR amplification of genomic DNA of 5 healthy domestic shorthair cats indicated the presence of 3 synonymous missense single-nucleotide polymorphisms (SNP) and 1 nonsynonymous missense SNP, which changed an amino acid from arginine to proline.
The alignments obtained from each of the 8 programs were compared to the corresponding reference alignments.
Local multiz alignments obtained from the PromAn server [74] were exclusively used for the promoter region of Hsp68 to define the TSS in each species.
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