The sequences obtained from the patients were compared with the wild type sequence by NCBI nucleotide blast online software (http://blast.ncbi.nlm.nih.gov/Blast.cgi).nih.gov/Blast.cgi
BLAST searches were performed for all sequences via interrogating GenBank's online nucleotide database using the megablast algorithm.
Forty-five loci were selected and sequences compared to previously published data using the online nucleotide BLAST tool of the National Center for Biotechnology Information (Altschul et al., 1990).
Furthermore, the recovery of this signal is impeded by lineage-specific rate heterogeneities (supplementary table 1, Supplementary Material online), nucleotide composition biases (fig. 1), and strand asymmetrical properties (fig. 3).
The obtained DNA sequences were analyzed using a BLASTx search of the in-house Burkholderia pan-genome databases and by a BLASTn search against the NCBI online nucleotide collection (nr/nt) database to confirm their identities.
In three cases we could identify a homolog in rodent that presented a conserved exon-exon boundary (>85% identity over at least 60 nucleotides, see supporting online material).
Protein alignments were converted into nucleotide alignments using the online PAL2NAL server (http://www.bork.embl.de/pal2nal/) [38].de/pal2nal/
The complete nucleotide alignment is deposited online at [ 78].
The complete nucleotide alignment is available online at [ 79].
The complete nucleotide alignment is available online at Chloroplast Genome Database [ 90].
