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 Sequin 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
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.|
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]".|
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
CDS Flags (combine any of the following letters):
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 the Discrepancy Report page for information about its output.|
Master Genome Flags (combine any of the following letters):
Example Command Lines:
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"):
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.
>Sc_16 [organism=Saccharomyces cerevisiae] tataggcgaatcgagtatattattttttctcaacatatgtat atgaacatgagaatatatttataggaatgtataaaattgtga cctctcctgctattttagttactgattttatgtatgtagggg gaataggggctgcctttcttaatgcagttttaattttttctt ttaattttttcttagtaaaattatttaaagtaaagattaatg gaataaccattgcgcttttttttacagtttttggtttttcat tttttggaaaaaatattttaaatattttacctttttatttag ggggtattttatatagtatctatacttcaacagatttttctg aacatatagttcctattgctttttcaagtgcattagcccctt ttgtaagcagtgttgctttttatggagaaatatcctatgaaa catcatatataaatgcaattttaattggtattttaattggtt ttatagtggttcctttgtctaaaagtctttatgactttcatg agggatatgatttatataatttaggttttacagcaggtt
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
>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...
>WS1030 [gene=sde3p] [protein=SDE3P] MYKIVTSPAILVTDFMYVGGIGAAFLNAVLIFSFNFFL VKLFKVKINGITIAAFFTVFGFSFFGKNILNILPFYLG GILYSIYTSTDFSEHIVPIAFSSALAPFVSSVAFYGEI SYETSYINAILIGILIGFIVVPLSKSLYDFHEGYDLYN LGFTAG
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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Last updated: 2017-08-17T11:09:51-04:00