General Directions for GenBank Flat File Format
GenBank records are commonly presented in GenBank Flat File Format which provides general information and annotations of a sequence, followed by the sequence itself. (GenBank also supports FASTA format which is more commonly used.)
Please make note of the following:
- mthap looks only at the sequence part, not any part of the header.
- mthap will ignore any sequence lines which have any non-nucleotide characters (not including position and spaces).
- Heteroplasmy should use the single letter format: Y, not [C/T].
- All "N" nucleotides will be ignored to handle the 3107N convention; this is not currently positional. Some incomplete GenBank sequences use N for unsequenced regions.
- The sequence must contain a complete mtDNA sequence. Incomplete sequences may result in strange results.
- Handling of insertions/deletions may vary from other conventions. Please keep this in mind when interpreting the results.
- Alignment will take a few extra seconds depending on the complexity of the sequence. Please be patient.
- Go to GenBank.
- Find an mtDNA sequence you want. (Search "Nucleotide" for the sequence ID, or "homo sapiens mitochodrion" or use my sequence.)
- Copy the text starting with the "LOCUS" line and ending in "//". At minimum you need everything between "ORIGIN" and "//".
- Save the text somewhere on your computer.
- Click on the "Browse" button on the mthap page and select the text file.
- Click on "Upload."