Protein-coding and ribosomal RNA genes were firstly identified using BLAST searches at GenBank, and then by alignment with previously published mt genomes from species of Crassostrea, Mytilus and other closely related mollusks [ 33].
Finally, a random subset of the contigs, which represented a variety of length and read coverage, were validated by direct alignment to previously published, Sanger sequenced, full-length Eucalyptus genes that were directly cloned from cDNA (Additional File 3).
Treatment with GM6001 at 100 μM did not change the extent of resorbed bone area compared with the area associated with vehicle-treated cells, which is in alignment with previously published data [ 13].
Alignment of previously published sequences for the structural gene region (223 codons of prM/E) (14 ) showed that 8 of the 10 older Pará strains had one or more mutations within the fusion peptide of the E protein that is highly conserved among all flaviviruses; it is located in domain II (E98 E110) and plays a role in mediating the acid-catalyzed fusion of virions with target cell membranes (22 ).
Sequences from Ministeria vibrans and publicly available sequences from the nr- and dbEST databases (http://www.ncbi.nlm.nih.gov/blast/blast_databases.shtml) were retrieved from BLAST results and aligned to a previously published alignment [33] using the Mafft program [34].
To have a control, we also generated the reciprocal best net alignment between the previously published peregrine falcon assembly [ 61] and zebra finch assembly.
(1) New sequences were manually added and aligned to the previously published [ 4] multiple alignement using the BioEdit sequence alignment editor [ 31].
The 5' primer E0364 (GCG GAG CTC GAG TTA AGA GRA TAG ARA ACA, where R = A/G) was designed based on previously published alignment of the MADS domain from several plant species, including Gerbera [ 4, 74].
Primers LR1 and NDL22 were designed from previously published alignments of the large ribosomal subunit [66] flanking the variable domains D1 and D2.
First, data for the five new extant genera sampled here (Canis, Felis, Nandinia, Ailurus, Erinaceus) were added to our previously published alignments; four mitochondrial genomes and information from 31 nuclear loci at the Genbank database were added to the overall matrix.
