In the case of the detection by Blast of only a few homologs for a gene of interest, an alignment analysis showing more homology with genes/proteins of distant species than to a closer one indicates a horizontal transfer event for this gene.
After an alignment analysis with the legume Vigna radiata chloroplast genome, 56 contigs composed of 59,040 bp were generated, spanning a total of 129,208 bp that belong to the Prosopis cp genome.
To investigate sequence similarities between L. santarosai serovar Shermani strain LT821 and strain CCF, we examined the conservation of genes in an isolate of L. santarosai serovar Shermani genome and a sequence alignment analysis by using a VectorNTI tool.
A multiple alignment analysis on the Bordetella repeats shows a high level of conservation within the genus, as well as more widely within the all Betaproteobacteria class.
To examine the evolutionary relationship of the putative MuERVs identified in this study, a phylogenetic tree of RT sequences was constructed following a multiple alignment analysis.
A multiple alignment analysis was carried out on AP2 domain sequences from Hevea, Arabidopsis and Populus.
ConTra is a promoter alignment analysis tool for identification of transcription factor binding sites across species.
A multiple alignment analysis was performed on full-length AP2 domain sequences from Hevea, Arabidopsis and Gossypium.
We performed a multiple alignment analysis of the deduced amino acid sequences [ 29] (see Supplementary Figure S1 in Supplementary Material available online at http://dx.doi.org/10.1155/2014/424767).org/10.1155/2014/424767
A multiple alignment analysis of the amino acid sequences of the 41 proteins was then performed, focusing on the ligand-binding and DNA-binding domains (fig. 4).
