PrimerMiner v0.22

• BOLD v4 API is no longer working, had to update to v5. This now requires a API key you can find in your bold account.
• Now allows to subset the number of reads downloaded per group from BOLD.
• Gives better feedback what taxa data is currently downloaded.

PrimerMiner v0.21

• Now allows subsetting number of mitogenomes to be downloaded.
• Now reports the number of sequences and mitogenomes detected before downloading them.
• Minor bug fixes related to subsetting and mitogenome sequence extraction.

PrimerMiner v0.20

• Minor bug fix related to sequence subsetting

PrimerMiner v0.19

• Now allows for randomly subsetting GB downloads using the option GB_subset = 5000. This is useful when targeting large groups, where thousands of additional sequences do not add any novel information.

PrimerMiner v0.18

• Bug fix: In rare cases where no sequences are obtained with Download_GB() PrimerMiner could crash. Now fixed!

PrimerMiner v0.17

• Added new function primerversions() that generates all possible primer version contained in a degenerated primer.

PrimerMiner v0.16

Fixes a recently introduced error with NCBI which prevented sequences to be downloaded (due to new API restrictions). Now using web history to download sequences.

PrimerMiner v0.15

• In the primer evaluation, results tables are returned now directly to the console if no file name is provided evaluate_primer(save=NULL). Allows for direct processing of the information in R.
• Improved detection of gene annotations fro mitochondrial genomes! Now also the second line at the respective region is evaluated should the first one yield no results. "gene", "CDS" and "rRNA" are phrased, but make sure to cover all possible spelling variants of a marker.

PrimerMiner v0.14

The evaluate_primer output table now includes template sequence names as provided in the fasta file (sequ_names = T).

PrimerMiner v0.13

The scoring tables for mismatch type and position are now integrated into PrimerMiner and have no longer be provided when evaluating primers!

This means that with evaluate_primer(..., mm_position ="Position_v1", mm_type="Type_v1") PrimerMiner uses the default scoring tables integrated in the package. For publications, you can simply mention that the default scoring tables where used.