Contents 1 Default Settings in SeqSphere+ version 1.0.0 1.1 Query Thresholds 1.2 Blast Settings 1.3 Reference Genome Filter 1.4 Query Genome Filter

Default Settings in SeqSphere+ version 1.0.0

Query Thresholds

• Required gene identity found in query genome >= 90%
• Required gene overlap found in query genome >= 100%;

Blast Settings

• Word size: 11
• Mismatch penalty: -1
• Match reward: 1
• Gap open costs: 5
• Gap extension costs: 2;

Reference Genome Filter

• Minimum Length Filter

Filters all genes that are shorter than 50 bases.

• Start Codon Filter

Filters all genes that contain no start codon (ATG, GTG, TTG, ATT, or CTG) at the beginning of the gene.

• Stop Codon Filter

Filters all genes that contain no stop codon, more than 1 stop codon or if the stop codon is not at the end of the gene. Does not consider any GenBank annotations that indicate non-continous coding regions.

• Multi Copy Filter

Filters all genes that have fragments that occur in multiple copies in a genome (with identity >= 90% and more than 100 bases overlap.

• Gene Overlap Filter

If two genes overlap more than 4 bases, remove the shorter gene.

Query Genome Filter

• Stop Codon Percentage Filter

Filters all genes that fullfill the following condition in more than 80% of the query genomes: gene contains no stop codon, more than 1 stop codon or the stop codon is not at the end of the gene

Disabled Query Genome Filters: Start Codon Filter, Stop Codon Filter