Hi Remi,
I used MitoFinder 1.4.1. (singularity) to annotate mitochondrial genes from UCE library assemblies. I then used the script create_tbl2asn_files.py to generate sqn files for NCBI submission. However, when I ran table2asn (the updated version of tbl2asn) to validate my sequences, I got warnings like the following in the .val file:
Warning: valid [SEQ_FEAT.PartialProblemNotSpliceConsensus3Prime] 3' partial is not at end of sequence, gap, or consensus splice site FEATURE: CDS: NADH dehydrogenase subunit 4 <7> [lcl|NODE_1_length_16677_cov_24.806642:c6164-<4788] [lcl|NODE_1_length_16677_cov_24.806642: raw, dna len= 16677] -> [lcl|NODE_1_length_16677_cov_24.806642_4]
I only got one mitochondrial contig in this particular case and the length seems near complete. But I wonder if this warning indicates something wrong with my MitoFinder annotation. Could you shed some light on it? Thanks a lot!
Hi Remi, I used MitoFinder 1.4.1. (singularity) to annotate mitochondrial genes from UCE library assemblies. I then used the script create_tbl2asn_files.py to generate sqn files for NCBI submission. However, when I ran table2asn (the updated version of tbl2asn) to validate my sequences, I got warnings like the following in the .val file:
Warning: valid [SEQ_FEAT.PartialProblemNotSpliceConsensus3Prime] 3' partial is not at end of sequence, gap, or consensus splice site FEATURE: CDS: NADH dehydrogenase subunit 4 <7> [lcl|NODE_1_length_16677_cov_24.806642:c6164-<4788] [lcl|NODE_1_length_16677_cov_24.806642: raw, dna len= 16677] -> [lcl|NODE_1_length_16677_cov_24.806642_4]
I only got one mitochondrial contig in this particular case and the length seems near complete. But I wonder if this warning indicates something wrong with my MitoFinder annotation. Could you shed some light on it? Thanks a lot!
Best, Ling