Phylogenetic analysis using amino acid sequences allowed us to identify gene orthologs and clusters of orthologous groups for further characterizations.
The use of orthologous sequences allowed us to more accurately predict the main coding region and define the 5'-UTR that is necessary to identify conserved uORFs.
However, the use of entire precursor sequences allowed us to identify orthologs between species, despite differences in their mature miRNA regions.
The use of the KEGG Orthology (KO) system [ 42] to annotate sequences allowed us to draw pathway maps of the transcripts in our library using Arabidopsis graphs as templates.
Phylogenetic analyses of a dataset incorporating 30 new complete 18S rRNA tunicate sequences allowed us to compare for the first time the use of RNA-specific paired-site substitution models [ 29, 30, 34] and the CAT mixture model [ 31], relaxing the hypothesis of a uniform substitution process by letting patterns of substitution be distinct at different sites.
The use of colorspace coding of nucleic acid sequences allowed us to discard reads that were likely due to technical error during deep sequencing, enhancing the confidence in the remaining sequences.
The use of XFP fusions to TIP genomic sequences allowed us to investigate both the tissue specificity and the subcellular localisation of these proteins.
A match analysis with the Roma M-founder lineages using a database of more than 3,700 Indian sequences, allowed us to identify North-Western India, and specifically the Punjab region, as the putative homeland of the Roma Diaspora.
Genetic fusion of the M2e and hepatitis B virus core (HBc) coding sequences allowed us to obtain highly immunogenic virus-like particles.
The exponential accumulation of genomic sequences allowed us to study the evolution of the KLK gene family in different species.
The published genome sequence is based on strain A4, and so differences between the A91 and reference sequences allowed us to identify SNP markers for our population.
