Discriminating Probes Selection
Add adapters to probes
Annotate probes
Local BLAST
Calculate physical and chemical properties
Cut probes
Cut string into segments
Delete rows with duplicated values
Complement BLAST result
Read GISAID sequence file
Get GenInfo Identifier numbers
Get nucleotide sequences from NCBI
Get NCBI sequence record
Builds local database for BLAST
Create unique identification values
Normalize variable
Rate variables
Read and unite files
Read table file
Store data in SQLite database
Summarize BLAST result
Trim data frame
Assigns master record's id to all project records
Combine two data frames
Set of tools for molecular probes selection and design of a microarray, e.g. the assessment of physical and chemical properties, blast performance, selection according to sensitivity and selectivity. Methods used in package are described in: Lorenz R., Stephan H.B., Höner zu Siederdissen C. et al. (2011) <doi:10.1186/1748-7188-6-26>; Camacho C., Coulouris G., Avagyan V. et al. (2009) <doi:10.1186/1471-2105-10-421>.