Inter-population homoeologue alignment using allele size (Table 3) was, therefore, derived from identifying the homoeologue pairing that maximised the number of joining loci in agreement with the alignment (matches) while minimising the number of joining loci at variance with the alignment (mismatches).
Each annotation report page contains information about the gene or transcript assembly sequence, protein translation, BLAST alignments to proteins from UniRef and seven plant genomes, protein domain alignments, matches to KEGG orthologs with links to KEGG pathways, gene orthologous group results, SSR markers, predicted SNPs for PUT sequence assemblies and microarray probe matches.
Seventy-six percent of recombinant fragments in the M. canettii alignment matched most closely with STB-K and STB-J, suggesting that they originated from bacteria in these or related lineages.
Unlike previous methods, RAF's scoring model does not rely on ad hoc combinations of thermodynamic free energies for structural features (Mathews et al., 1999) with arbitrary alignment match and gap penalties (Hofacker et al., 2002), nor does RAF attempt the ambitious task of simultaneously modeling the evolutionary history of both sequences and structure (Knudsen and Hein, 2003).
Next, you can visually verify some of these sites to see if the raw alignments match up with these de novo hits.
The eye sockets, cheek bones and jaw alignment matched.
Alignment, matching, and map computation between geometric data sets.
A nucleotide alignment was matched with corresponding amino acids to produce a codon alignment using PAL2NAL [ 39] that resulted in 131 codons.
To eliminate false positive snoRNA genes, we used the following strategy – methylation sites generated from the above-mentioned alignment were matched with the sites predicted for putative snoRNA (identified using SNOSCAN) to generate a subset of relevant snoRNA genes (for matched methylation sites).
Results were filtered for alignments that matched with an e-value equal or lower than 10-5.
Uploaded alignments were matched with the reference species tree (Additional file 1) and F. olivaceus fixed as outgroup lineage if required.
