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1.  A 44K microarray dataset of the changing transcriptome in developing Atlantic salmon (Salmo salar L.) 
BMC Research Notes  2011;4:88.
Atlantic salmon (Salmo salar L.) is an environmentally and economically important organism and its gene content is reasonably well characterized. From a transcriptional standpoint, it is important to characterize the changes in gene expression over the course of unperturbed early development, from fertilization through to the parr stage.
S. salar samples were taken at 17 time points from 2 to 89 days post fertilization. Total RNA was extracted and cRNA was synthesized and hybridized to a newly developed 44K oligo salmonid microarray platform. Quantified results were subjected to preliminary data analysis and submitted to NCBI's Gene Expression Omnibus (GEO). Data can be found under the GEO accession number GSE25938.
Throughout the entire period of development, several thousand genes were found to be differentially regulated. This work represents the trancriptional characterization of a very large geneset that will be extremely valuable in further examination of the transcriptional changes in Atlantic salmon during the first few months of development. The expression profiles can help to annotate salmon genes in addition to being used as references against any number of experimental variables to which developing salmonids might be subjected.
PMCID: PMC3073910  PMID: 21447175
2.  KISSa: a strategy to build multiple sequence alignments from pairwise comparisons of very closely related sequences 
BMC Research Notes  2009;2:91.
The volume of viral genomic sequence data continues to increase rapidly. This is especially true for the smaller RNA viruses, which are relatively easy to sequence in large numbers. The data volumes cause a number of significant problems for research applications that require large multiple alignments of essentially complete genomes, which are of the order of 10 kb.
We present a simple strategy to enable the creation of large quasi-multiple sequence alignments from pairwise alignment data. This process is suitable for large, closely related sequences such as the polyproteins of dengue viruses, which need the insertion of very few indels.
The quasi-multiple sequence alignments generated by KISSa are sufficiently accurate to support tree-based genome selection for interactive bioinformatics analysis tools. The speed of this process is critical to providing an interactive experience for the user.
PMCID: PMC2694821  PMID: 19457259
3.  Sequence Searcher: A Java tool to perform regular expression and fuzzy searches of multiple DNA and protein sequences 
BMC Research Notes  2009;2:14.
Many sequence-searching tools have limiting factors for their use. For example, they may be platform specific, enforce restrictive size limits and sequences to be searched, or only allow searches of one of DNA or protein.
We present an easy-to-use, fast, platform-independent tool to search for amino acid or nucleotide patterns within one or many protein or nucleic acid sequences. The user can choose to search for regular expressions or perform a fuzzy search in which a particular number of errors is accepted during matching of a sequence. Positions of mismatches in fuzzy searches are displayed graphically the user.
SeqS provides an improved feature set and functions as a stand-alone tool or could be integrated into other bioinformatics platforms.
PMCID: PMC2637886  PMID: 19183477

Results 1-3 (3)