The resulting profile HMMs (or consensus protein sequences created from them) can be used to search EST databases with software such as the Wise2 package [ 53].
While genetically modified organisms have had their DNA sequences changed, typically by having traits of another species spliced in with their own, synthetic biology, or simply "synbio," involves the creation of entirely new organisms with DNA sequences created from whole cloth on a computer.
Primers were designed using an in-house database of Musa EST sequences created from available on-line GenBank sequences and a 3' EST database donated to the Global Musa Genomics Consortium by Syngenta.
E-genotyping is a novel in silico method to survey mapped read sequence data using 31bp probe sequences created from a list of known or suspected SNPs.
IHAT performs a PSI-BLAST search using a checkfile derived from a custom HMM and consensus sequence created from all members associated with a particular Clustered Orthologous Group (COG) [39] within the STRING database [40] (Figure 2).
Subsequent CLUSTALW alignment of the sequence from LyTASK to the sequence profile (created from the sequences of the two templates 3UKM and 3UM7) also demonstrates reasonable sequence similarity.
All possible CATG + 17-nt tag sequences were created from the Sus scrofa genome sequence (Sscrofa9.2) and UniGene (NCBI36.1, 20090827) databases and used as reference sequences to align and identify the sequencing tags.
The HM database of expressed peptide sequences was created from the most extensive healthy human-microbial distal gut metaproteome available to date.
A reference sequence was created from the D. pulex genome sequence [ 18] for each of the Ldh genes indicating the location of exons, introns and the start and stop codons.
A sequence logo created from the alignment of full-length zebrafish OlfC amino acid sequences highlights a number of conserved motifs among members of the family.
