The annotated nucleotide sequence of the B. rhizoxinica genome has been deposited in the EMBL database under the following accession numbers: EMBL: FR687359 (Burkholderia rhizoxinica HKI-0454, complete genome), EMBL: FR687360 (Burkholderia rhizoxinica HKI-0454 pBRH01d pBRH01, complete sequence), EMBL: FR687361 (Burkholderia rhizoxinica HKI-0454 pBRH02d pBRH02, complete sequence).
We extracted sequences of the core genes from.fna files (files that include annotated nucleotide sequences of all genes in the given organism) of the investigated strains and aligned them using MUSCLE (Edgar 2004) with default parameters.
Annotated nucleotide using blast2go from the pacu slow and fast muscle transcriptome.
By June 2010, 5293 proteins in PDB were annotated "nucleotide binding," and nucleotides constitute ~15% of biologically relevant ligands [ 8].
Secondly, all IS annotated nucleotide sequences, in total 3377 in July 2012, were downloaded from the ISfinder site [ 28], a web repository of known ISs.
Annotated nucleotide sequences of the regions identified in these 73 contigs as containing A-domains and/or NRPS associated genes are provided in Additional file 7. On the basis of the draft genome sequence of strain BAI3, three scaffold DNA sequences were identified as belonging to META-B.
That way, every nucleotide sequence can be annotated, regardless of the actual reading frame or even a shift of the frame.
An integrated database system is used for data fusion of annotated nucleotide and amino acid sequences together with evidenced transcriptional regulatory relationships and corresponding sequence features.
Thus, for all 450 k probes, we annotated the number of nucleotides at the intended site of hybridization that mapped to repetitive DNA based on RepeatMasker (http://www.repeatmasker.org; RepeatMasker, Institute for Systems Biology, Seattle, WA, USA) annotation in BLAT [ 30].
3′UTR forms were assigned by overlaying annotated Flybase UTR forms with 3Pseq reads lying within 200 nucleotides of the annotated 3′UTR end.
