Preparing a Source Modifiers Table File for All Source Modifiers

BankIt accepts source modifiers (e.g. specimen voucher and isolate) in two ways, as a tab-delimited text file containing a Source Modifiers Table (as described below) or by applying the same source modifier value to all sequences in the submission using the input form. Source modifiers can be changed by uploading new tables to overwrite a previous table or by correcting or removing a previously input value in the form. The current values of all source modifiers appear at the bottom of the page.

It is recommended for multiple sequences that you use only a table file that contains all the source modifiers you want to add and that you do not add source modifiers using both a table and the input value forms.

Setting up the Source Modifiers Table

The Source Modifiers Table is a tab-delimited text file of the source modifiers for all specimens in a BankIt set.

The following modifiers must have only 'TRUE' as the value reported in a source modifier table when they are used:

See below for an annotated list of source modifiers

Contents of the Source Modifiers Table

The first row in the table contains the labels for each column. Each column in the table is a different source modifier. See below for the complete list of source modifiers.

The first column contains the Sequence_IDs used to identify each sequence in the nucleotide FASTA file.

Specimens are identified in the Source Modifiers Table by the same Sequence_ID used in the FASTA file.

The heading for the first column must be exactly Sequence_ID as shown in the sample below.

Each specimen in the set must have a line in the source modifiers file, even if there are no modifiers to apply to the specimen.

Each Sequence_ID may appear only once in the source modifier file.

Shown below are the contents of a Sample Source Modifiers Table file. Right-click on the link to save as a tab-delimited text file.

Sequence_ID Collected_by Collection_date Country Isolation_source Isolate Lat_Lon Specimen_voucher
Seq1 C. Grant 31-Jan-2001 USA soil A 13.57 N 24.68 W MKP 334
Seq2 S. Tracy 28-Feb-2002 Slovakia contaminated soil B 13.24 N 24.35 W MKP 1230
Seq3 A. Gardner 16-Apr-2001 France farm soil C 43.21 N 56.78 W 1B-2526
Seq4 F. McMurray 26-May-2002 Germany farm runoff water D 45.32 N 21.34 E WBM 86-64
Seq5 V. Leigh 13-Jun-2003 Brazil forest soil E 46.80 N 13.57 E 1B-2518
Seq6 E. Flynn 15-Aug-2000 Australia river water F 68.53 S 57.42 E WBM 86-65
Seq7 G. Kelly 26-Oct-2002 Mexico river bed soil G 22.44 S 55.77 W 1B-2355

Saving the Source Modifiers Table

When using a spreadsheet program, be sure to save your file as tab-delimited text. If you are not sure that the "Save" option in your program
will do this for you, use "Save As..."

In Excel, select "Save As..." from the File menu. In the "Save as type:" pull-down menu, select "Text (Tab delimited) (*.txt)."

Source Modifiers

Commonly used Source Modifiers

The following source modifiers are available to further describe the sequences in a BankIt set: