BankIt Submission Help: Nucleotide FASTA

• Use a text editor (for example, WordPad) to prepare a file containing the set of nucleotide sequences in FASTA format.
• Be sure to save your file as Plain text or Text document.
• If you are not sure that the "Save" option in your program will do this , use "Save As...". In the "Save as type:" pull-down menu, select "Text Document"
• If using Word, select "Save As.." from the File menu. In the "Save as type:" pull-down menu, select "Plain Text(*.txt)."
• Do not save the file as .doc or .rtf (rich text format)

• Each sequence in the set contains a FASTA definition line followed by the raw sequence data.
• The definition line for each sequence begins with a ">" followed by a Sequence_ID. The Sequence_ID identifies the same specimen in all the steps of a submission (for example, nucleotide FASTA file, protein FASTA file, Source Modifier file, etc). Sequence_IDs must be unique within the set and may not contain spaces.
• The Sequence_ID must be followed by a space.
• It is strongly recommended that the definition line also include the organism name, which must be in this format: [organism=Organism name]. If organism names are not input as part of their FASTA definition lines, they must be provided in an Organism table in the next step of the submission process.
• For Barcode submissions, the definition line MUST contain the organism name for the sequence after the Sequence_ID.
• The organism name must be specified in exactly the format shown in the samples: [organism=Organism name]
• The FASTA definition line must be one line and may not contain any internal hard returns.
• The FASTA definition line must be separated from the actual sequence by a hard return.

Be aware that the placement of spaces and hard returns within a FASTA format is critical for the FASTA information and sequence(s) to be read correctly:

Sample definition line and sequences

>Seq1 [organism=Carpodacus mexicanus] C.mexicanus clone 6b actin (act) mRNA, partial cds
CCTTTATCTAATCTTTGGAGCATGAGCTGGCATAGTTGGAACCGCCCTCAGCCTCCTCATCCGTGCAGAA
CTTGGACAACCTGGAACTCTTCTAGGAGACGACCAAATTTACAATGTAATCGTCACTGCCCACGCCTTCG
TAATAATTTTCTTTATAGTAATACCAATCATGATCGGTGGTTTCGGAAACTGACTAGTCCCACTCATAAT
CGGCGCCCCCGACATAGCATTCCCCCGTATAAACAACATAAGCTTCTGACTACTTCCCCCATCATTTCTT
TTACTTCTAGCATCCTCCACAGTAGAAGCTGGAGCAGGAACAGGGTGAACAGTATATCCCCCTCTCGCTG
GTAACCTAGCCCATGCCGGTGCTTCAGTAGACCTAGCCATCTTCTCCCTCCACTTAGCAGGTGTTTCCTC
TATCCTAGGTGCTATTAACTTTATTACAACCGCCATCAACATAAAACCCCCAACCCTCTCCCAATACCAA
ACCCCCCTATTCGTATGATCAGTCCTTATTACCGCCGTCCTTCTCCTACTCTCTCTCCCAGTCCTCGCTG
CTGGCATTACTATACTACTAACAGACCGAAACCTAAACACTACGTTCTTTGACCCAGCTGGAGGAGGAGA
CCCAGTCCTGTACCAACACCTCTTCTGATTCTTCGGCCATCCAGAAGTCTATATCCTCATTTTAC


>Seq2 [organism=Vireo solitarius] Vireo solitaries isolate A actin (ACT) gene, complete cds
GGTAGGTACCGCCCTAAGNCTCCTAATCCGAGCAGAACTANGCCAACCCGGAGCCCTTCTGGGAGACGAC
CAAATCTACAACGTAGTCGTTACGGCCCACGCCTTCGTAATAATCTTTTTCATAGTAATGCCAATCATAA
TCGGAGGATTCGGGAACTGACTAGTTCCTCTAATGATTGGGGCCCCAGACATAGCATTCCCTCGAATAAA
CAACATAAGCTTTTGACTACTACCACCATCATTCCTACTCCTAATAGCCTCCTCAACAGTAGAAGCAGGA
GCCGGAACCGGATGAACCGTGTACCCACCACTAGCTGGAAACCTGGCCCACGCCGGAGCCTCAGTAGACC
TAGCTATCTTCTCCCTACACCTAGCAGGTATCTCATCCATCCTGGGGGCAATTAACTTCATTACAACAGC
AATCAACATAAAACCACCCGCCCTCTCACAATACCAAACACCACTATTCGTGTGATCCGTCCTAATTACG
GCCGTACTACTCCTACTATCTCTCCCAGTACTAGCCGCCGGTATCACCATGCTACTCACAGACCGCAACC
TCAACACCACCTTCTTTGACCCAGCAGGAGGAGGAGACCCAGTACTATACCAGCACCTATTCTGATTCTT
CGGACACCCAGAAGTCTACATCCTAATTCTC

Sample nucleotide FASTA

sample file