Expand description
Node management and scoring for gene prediction
This module contains all functionality related to creating, scoring, and managing gene prediction nodes. Nodes represent potential start and stop codons in the sequence and are used in dynamic programming to find optimal gene predictions.
Functionsยง
- add_
nodes - Add nodes for start and stop codons in both directions
- calc_
orf_ gc - calculate_
dicodon_ gene - Calculate dicodon (6-mer) frequencies in genes and store log likelihood scores relative to background frequencies in the training structure.
- find_
best_ upstream_ motif - Find the highest scoring motif/spacer combination for a node.
- intergenic_
mod - Calculate intergenic modification score for operons and overlaps
- raw_
coding_ score - Calculate raw coding scores
- rbs_
score - RBS Scoring Function: Calculate the RBS motif and then multiply it by the appropriate weight for that motif (determined in the start training function).
- record_
gc_ bias - Record GC bias for training
- record_
overlapping_ starts - reset_
node_ scores - Reset all scoring data for nodes to default values
- score_
nodes - Score nodes for gene finding
- sort_
nodes_ by_ position - Sort nodes by genomic position with strand ordering