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.

Brief directions:

1. Go to GenBank.
2. Find an mtDNA sequence you want. (Search "Nucleotide" for the sequence ID, or "homo sapiens mitochodrion" or use my sequence.)
3. Copy the text starting with the "LOCUS" line and ending in "//". At minimum you need everything between "ORIGIN" and "//".
4. Save the text somewhere on your computer.
5. Click on the "Browse" button on the mthap page and select the text file.
6. Click on "Upload."