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 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.
NEW:Use version 19.2 or higher, to ensure proper handling of EC numbers, based on ExPASy's ENZYME nomenclature database. For each .fsa file an output .ecn file is generated with a table of changes that will be made to out-of-date EC numbers, during processing of the submission at NCBI.
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 a Sequin 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:
tbl2asn command line 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.
- s :FASTA Set (s Batch, s1 Pop, s2 Phy, s3 Mut, s4 Eco)
- l :FASTA+Gap Alignment
- z :FASTA with Gap Lines
- e :PHRAP/ACE
- d :FASTA Delta, di FASTA Delta with Implicit Gaps
- a :Any (default)
-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):
- v :Validates the data records. The output is saved to files with a .val suffix. A summary file named errorlog.val is also created with the number, severity and type of errors found in all the .val files.
- b :Generates GenBank flatfiles with a .gbf suffix.
- r :Validates without Country Check
Sample command line: -V vb
-k CDS Flags (combine any of the following letters):- c :Instructs tbl2asn to annotate the longest open reading frame (ORF) if a .tbl file is not provided. The product name will be 'unknown' unless a product name is included in the FASTA definition, [product=xyz].
- m :Allows alternative start codons to be used in ORF searches.
- r :Allows Runon ORFs
-c Cleanup (combine any of the following letters):
- f :Fix product names in specific categories of the Discrepancy Report. The output of changed product names is saved to files with a .fixedproducts suffix.
- x :Extend partial ends of features by one or two nucleotides to abut gaps or sequence ends.
- D :Correct Collection Dates (assume day first)
- d :Correct Collection Dates (assume month first)
-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.
-M Master Genome Flags (combine any of the following letters):
- n :Normal. Combines flags for genomes submissions (replaces -a s -V v -c f; invokes FATAL calls when -Z discrep is included).
- b :Big. Combines flags for genome submissions with >20,000 contigs (like 'n' but uses the 'big' version for -Z discrep).
- p :Power users. Combines flags for genomes submissions (like 'n' but invokes the power-user FATAL calls for -Z discrep).
- t :TSA. Combines flags for TSA submissions (replaces -a s -V v -c f; invokes TSA-specific validations)
Example Command Lines:
- tbl2asn -t template.sbt -p path_to_files -V v
- tbl2asn -t template.sbt -p path_to_files -a s -V v
- tbl2asn -t template.sbt -i x.fsa -V v
- tbl2asn -t template.sbt -p path_to_files -M n -Z discrep
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 Create Submission Template page
- Fill in the boxes
- Click on "Create Template"
- SAVE the file as template.sbt
OR
- Choose start a new submission with Sequin.
- Enter manuscript title if desired.
- Enter contact, authors and affiliation information.
- Return to submission tab and use File->Export Submitter Info.
- Save as template.sbt.
Nucleotide sequence and FASTA defline formats (.fsa)
- SeqID (sequence identifier) which is the text between the '>' and the first space.
- 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:
- strain [strain=S288C]
- isolate [isolate=CWS1]
- chromosome [chromosome=XVI]
- 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]
Here is the list of source modifiers . See the Tax Browser for the genetic code values.
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.
- The quality scores appear below the sequence in the .sqn file, and are shown in the Quality format option when the .sqn file is viewed in Sequin.
>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
Tbl2asn Update Notification
To receive email notification about updates to tbl2asn, as well as a description of what is included in the update follow these directions .
