Please use the updated table2asn to access new features and the latest validations
What is tbl2asn?
Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Genome Workbench but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank. Additional manual editing is not required before submission.
Tbl2asn is available by anonymous FTP. Copy the right version for your platform, then uncompress the file, rename it to "tbl2asn", and set the permissions, as necessary for the platform.
Additional details are provided in the GenBank Submission Handbook
6 types of input data files
REQUIRED
- Template file containing a text ASN.1 Submit-block object (suffix .sbt).
- Nucleotide sequence data in FASTA format (suffix .fsa).
- Feature Table (suffix .tbl). [Required only if including annotation]
OPTIONAL
- Quality Scores (suffix .qvl.)
- Protein sequence (suffix .pep). (These are rarely needed.)
- Source Table (suffix .src.)
Generating the .sqn file for submission
- The minimum requirements to generate an ASN .sqn file using tbl2asn are one .sbt file and one or more .fsa files.
- The files are placed in a source directory and a series of command-line arguments are used to generate the .sqn files.
- Tbl2asn will generate a .sqn for every .fsa file in the directory, plus any of the corresponding optional files that may be present. The other files must have the same file name prefix as their corresponding .fsa. (for example helicase.fsa and helicase.tbl).
Command Line Arguments
Typing "tbl2asn -" will give the full list of command line arguments. Here is a partial list of commonly used arguments:
| -p | Path to the directory. If files are in the current directory -p. should be used. |
| -r | Path for the resulting .sqn file(s) (if the -r argument is not used, the .sqn files will be saved in the source directory). |
| -t | Specifies the template file (.sbt). If the .sbt file is in a different directory the full path must be specified. |
| -i | Creates single submission from indicated .fsa file in a directory of multiple .fsa files. |
| -a | Specifies the File type.
|
| -j | Allows the addition of source qualifiers that will be the same for each submission. Example: -j "[organism=Saccharomyces cerevisiae] [strain=S288C]". |
| -V |
Verification (combine any of the following letters): A summary file named errorlog.val is also created with the number, severity and type of errors found in all the .val files.
Sample command line: -V vb |
| -k | CDS Flags (combine any of the following letters):
|
| -c | Cleanup (combine any of the following letters):
|
| -y | Adds a COMMENT to each submission. Example: -y "Contigs larger than 2kb have been annotated, representing approx. 87% of the total genome". |
| -Y | Like -y, but adds a COMMENT to each submission from a file. |
| -Z | Runs the Discrepancy Report. Must supply an output file name. Recommended only for annotated genome submissions, complete or WGS. See theDiscrepancy Report pagefor information about its output. |
| -M | Master Genome Flags (combine any of the following letters):
|
Example Command Lines
- Single non-genome submission: a particular .fsa file, and only 1 sequence in the .fsa file:
tbl2asn -t template.sbt -i x.fsa -V v
- Batch non-genome submission: a directory that contains .fsa files, and multiple sequences per file:
tbl2asn -t template.sbt -p path_to_files -a s -V v
- Genome submission: a directory that contains multiple .fsa files of a single genome, and one or more sequences per file:
tbl2asn -t template.sbt -p path_to_files -M n -Z discrep
- Genome submission for the most common gapped situation (= runs of 10
or more Ns represent a gap, and there are no gaps of completely
unknown size, and the evidence for linkage across the gaps is
"paired-ends"):
tbl2asn -t template -p path_to_files -M n -Z discrep -a r10k -l paired-ends
Before submitting your .sqn files to GenBank, review the .val
files and correct any error-level errors. Taxonomy-related errors
about missing lineages can generally be ignored. However, if there
is annotation and the genetic code is not the standard code, then
include the correct code in the .fsa definition line as shown in the
.fsa definition line , or with the -j in the command line,
to avoid errors.
Creating the template file (.sbt)
- Go to the Create Submission Template page
- Fill in the boxes
- Click on "Create Template"
- SAVE the file as
template.sbt
Nucleotide sequence and FASTA defline formats (.fsa)
- No size limit on nucleotide sequence, generally.
- FASTA file should consist of a single definition line beginning with a '>'.
- Minimum requirements for the FASTA defline are:
- SeqID (sequence identifier) which is the text between the '>' and the first space. The SeqIDs limits are:
- Must be <50 characters
- Can only include letters, digits, hyphens (-), underscores (_), periods (.), colons (:), asterisks (*), and number signs (#).
- Organism and related information (unless organism information is included with -j at the command line or in a .src file )
- Optional defline information is in this list of source modifiers and includes:
- SeqID (sequence identifier) which is the text between the '>' and the first space. The SeqIDs limits are:
Here is the list of source modifiers. See the Taxonomy pages for the genetic code values.
Biological
- strain
[strain=S288C] - isolate
[isolate=CWS1] - chromosome
[chromosome=XVI]
Other elements
- topology
[topology=circular] - location
[location=mitochondrion] - molecule
[moltype=mRNA](DNA is the default) - technique
[tech=wgs] - protein name
[protein=helicase](if using -c) - genetic code
[gcode=4]
Example FASTA
>Sc_16 [organism=Saccharomyces cerevisiae]
tataggcgaatcgagtatattattttttctcaacatatgtat
atgaacatgagaatatatttataggaatgtataaaattgtga
cctctcctgctattttagttactgattttatgtatgtagggg
gaataggggctgcctttcttaatgcagttttaattttttctt
ttaattttttcttagtaaaattatttaaagtaaagattaatg
gaataaccattgcgcttttttttacagtttttggtttttcat
tttttggaaaaaatattttaaatattttacctttttatttag
ggggtattttatatagtatctatacttcaacagatttttctg
aacatatagttcctattgctttttcaagtgcattagcccctt
ttgtaagcagtgttgctttttatggagaaatatcctatgaaa
catcatatataaatgcaattttaattggtattttaattggtt
ttatagtggttcctttgtctaaaagtctttatgactttcatg
agggatatgatttatataatttaggttttacagcaggtt
Feature table format (.tbl)
tbl2asn reads features from a five-column tab-delimited table called a Feature table. The feature table specifies the location and type of each feature. tbl2asn will process the feature intervals and translate any CDSs into proteins. The first line of the table should contain the following information:
>Features SeqID table_name
The SeqID must match the nucleotide sequence SeqID in the corresponding .fsa file.
Example Feature Table
>Feature Sc_16 Table1
69 543 gene
gene sde3p
69 543 CDS
product SDE3P
protein_id WS1030
Quality scores table format (.qvl)
- Provides Phrap/Consed quality scores.
- Has a defline with the corresponding SeqID from the .fsa file.
- Generates Seq-graph data that will be included with the nucleotide sequence of the .fsa file in the final .sqn file.
>Sc_16 51 63 70 82 82 82 90 90 90 90 86 86 86 86 86 86 90 90 90 90 90 86 86 78...
Protein sequence format (.pep)
- This file is not usually needed because GenBank generally presents on the conceptual translation of the nucleotide sequence, which will be automatically generated by tbl2asn.
- This file will substitute the automatically translated products of the CDS features with the provided protein sequences, so is only needed in unusual cases.
- It is FASTA file of the protein sequence, where the SeqID must match protein_id in the .tbl file
Example FASTA
>WS1030 [gene=sde3p] [protein=SDE3P]
MYKIVTSPAILVTDFMYVGGIGAAFLNAVLIFSFNFFL
VKLFKVKINGITIAAFFTVFGFSFFGKNILNILPFYLG
GILYSIYTSTDFSEHIVPIAFSSALAPFVSSVAFYGEI
SYETSYINAILIGILIGFIVVPLSKSLYDFHEGYDLYN
LGFTAG
Source table format (.src)
For sets of sequences, especially those with different sources, a tab-delimited source modifier table file can be created, with a name that has a .src extension. The first column in the file must be the SeqIDs of the sequences. The first row gives the names of the source qualifiers being added, separated by tabs. Any additional rows list the SeqID and source qualifiers for each sequence in the corresponding .fsa file.
SeqID organism strain isolate
Sc_16 Zea mays A69Y JH90.6-2x12
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