Mitochondrial COI Sequence for GenBank Submission
Budget: $100 – $200 USD
I am looking for an experienced person to process 18 unassembled mitochondrial COI/cox1 Sanger sequence sets for GenBank submission.
The sequences are from digenean trematodes, probably Diplostomum spp. (Platyhelminthes: Trematoda). The current COI submission was rejected by GenBank because of possible frameshift warnings, so I need someone who can work with raw Sanger chromatograms, not only FASTA files.
I will provide:
raw .ab1 chromatogram files for forward and reverse reads,
current FASTA files,
primer sequences,
GenBank validation report with frameshift warnings.
Required work:
Inspect raw .ab1 chromatograms for all forward and reverse reads.
Trim low-quality ends and remove primer sequences.
Assemble forward and reverse reads into reliable consensus sequences.
Export only high-quality consensus regions, preferably regions supported by both reads.
Check ambiguous bases, double peaks, possible sequencing errors and problematic regions.
Translate the COI/cox1 sequences using the correct mitochondrial genetic code for the taxon.
Check for internal stop codons and frameshifts.
Prepare clean partial COI/cox1 sequences suitable for GenBank submission.
Provide a short summary table/report explaining what was done for each sequence and which sequences, if any, are too poor-quality to submit.
Important: Please do not manually delete or add nucleotides only to force the reading frame unless this is clearly supported by the chromatogram data. I prefer shorter, reliable partial COI sequences over longer sequences containing uncertain regions.
Final deliverables:
cleaned consensus sequences in FASTA format,
assembled files/project files if available,
a summary table/report for all 18 sequence sets,
notes about any sequences that cannot be confidently corrected.
Please apply only if you have previous experience with:
Sanger chromatogram analysis,
.ab1 files,
forward/reverse read assembly,
mitochondrial COI/cox1 sequences,
frameshift/stop codon checking,
GenBank sequence preparation.
The sequences are from digenean trematodes, probably Diplostomum spp. (Platyhelminthes: Trematoda). The current COI submission was rejected by GenBank because of possible frameshift warnings, so I need someone who can work with raw Sanger chromatograms, not only FASTA files.
I will provide:
raw .ab1 chromatogram files for forward and reverse reads,
current FASTA files,
primer sequences,
GenBank validation report with frameshift warnings.
Required work:
Inspect raw .ab1 chromatograms for all forward and reverse reads.
Trim low-quality ends and remove primer sequences.
Assemble forward and reverse reads into reliable consensus sequences.
Export only high-quality consensus regions, preferably regions supported by both reads.
Check ambiguous bases, double peaks, possible sequencing errors and problematic regions.
Translate the COI/cox1 sequences using the correct mitochondrial genetic code for the taxon.
Check for internal stop codons and frameshifts.
Prepare clean partial COI/cox1 sequences suitable for GenBank submission.
Provide a short summary table/report explaining what was done for each sequence and which sequences, if any, are too poor-quality to submit.
Important: Please do not manually delete or add nucleotides only to force the reading frame unless this is clearly supported by the chromatogram data. I prefer shorter, reliable partial COI sequences over longer sequences containing uncertain regions.
Final deliverables:
cleaned consensus sequences in FASTA format,
assembled files/project files if available,
a summary table/report for all 18 sequence sets,
notes about any sequences that cannot be confidently corrected.
Please apply only if you have previous experience with:
Sanger chromatogram analysis,
.ab1 files,
forward/reverse read assembly,
mitochondrial COI/cox1 sequences,
frameshift/stop codon checking,
GenBank sequence preparation.
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