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--- gene_prediction_find_supported_orfs [2025/08/18 15:12] – [find_supported_orfs.py in a nutshell] 134.190.145.228
+++ gene_prediction_find_supported_orfs [2025/08/18 15:53] (current) – 134.190.145.228
@@ Line 40: / Line 40: @@
 Currently, a high coverage region must be at least 150 bp in length to move on to the next stage
+{{ :high_cov_region.jpg?nolink |}}
 . High coverage regions are matched with supported introns and **spliced** accordingly
@@ Line 55: / Line 58: @@
 ===== Blastocystis =====
-Many Blastocystis lineages contain protein coding genes that do not end with a canonical STOP codon. Instead, a gene can end with 'T', 'TA', or 'TG'. Then, when the polyA tail is added during mRNA maturation, the STOP codon is completed.
+Many //Blastocystis// lineages contain protein coding genes that do not end with a canonical STOP codon. Instead, a gene can end with 'T', 'TA', or 'TG'. Then, when the polyA tail is added during mRNA maturation, the STOP codon is completed.
+Run of the mill gene predictors are unaware of this peculiarity, and will thus miss these genes. As some //Blastocystis// genomes can have up to 30-40% of such genes, this is a pretty major problem.
+find_supported_orfs.py integrates a nifty work-around to recognize such genes. The terminal 'T', 'TA' or 'TG' is part of a conserved TxxxxTGTTTGTT motif, where 'x' can be any base. The script will thus search for this motif in high coverage regions, and when found, change the sequence to TAAxxTGTTTGTT in-memory before passing it on to the ORF finder. Since now, the sequence does end with 'TAA', the ORF finder module will recognize the gene!
-Run of the mill gene predictors are unaware of this peculiarity, and will thus miss these genes. As some Blastocystis genomes can have up to 30-40% of such genes, this is a pretty major problem.
+Currently, only the last 50 bp of a high coverage region are search for this motif, and only the last instance of this motif is edited. This strictness was found to eliminate many false positive hits.
-find_supported_orfs.py integrates a nifty work-around to recognize such genes. The terminal 'T', 'TA' or 'TG' is part of a conserved TxxxxTGTTTGTT motif, where 'x' can be any base.