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Project Members:

• Alison Testa (admin)

[Alison Testa]

CodingQuarry v 1.3 updates:

• In previous versions the stop codon was not included as part of the CDS in the output GFF file. This is incorrect as per the GFF spec and has been corrected so that the stop codon is part of the CDS. This is now the expected format if you are supplying an annotations file for training (-a).

• The phase field in the GFF was also incorrect - this has now been fixed.

• A new parameter “-c” allows the user to supply a %GC content cut-off. Intergenic regions with a GC content below the cut-off are excluded from training. This is useful for running on genomes such as L. maculans to prevent training on AT-rich regions. Intended to be used after identifica- tion of repeat rich AT-rich regions has been performed. More information on this will be available soon with our AT-rich region identification software OcculterCut.

• Many thanks to those of you who have used CodingQuarry and offered your feedback and suggestions.

[Alison Testa]

CodingQuarry v 2.0 updates:
Released on the 9th of March 2016 with some minor changes and the introduction of “pathogen mode”:

• CodingQuarry-PM (pathogen mode) is a new run mode of CodingQuarry to assist in the prediction of effectors within fungal plant pathogen genomes (see manual).

• The nucleotide sequences of coding sequences are now output (out/Predicted_CDS.fa)

• Soft-masking (where repeats are indicated by lower case sequence letters in the FASTA genome
file) is now supported. See the Masking section in this manual for details.