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TBL2ASN AUTOMATED BULK SUBMISSION PROGRAM
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tbl2asn is a program that automates the submission of sequence records to
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GenBank. It uses many of the same functions as Sequin, but is driven
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entirely by data files, and records need no additional manual editing before
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submission. Entire genomes, consisting of many chromosomes with feature
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annotation, can be processed in seconds using this method.
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For a submission, tbl2asn expects a template file containing a text ASN.1
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Submit-block object. These can be easily generated in Sequin and saved for
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use by tbl2asn. The Submit-block contains contact information (to whom
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questions on the submission can be addressed) and a submission citation
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(which lists the authors who get scientific credit for the sequencing).
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The template file can also contain one or more text ASN.1 Seq-descr objects
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(such as Title or BioSource) appended after the Submit-block. These can
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also be generated in Sequin and saved to a file, and then appended to the
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template with a text editor. They will become descriptors packaged at the
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top of each submission file.
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tbl2asn reads five other kinds of data files. Nucleotide sequence data is
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expected in FASTA format, and these files are identified by having a .fsa
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suffix. Feature table files, in the five-column format described later,
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have a .tbl suffix. These can be easily generated by most genome centers
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that maintain feature locations in a spreadsheet or database. The protein
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translations of CDS features can also be supplied as FASTA sequences in
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files with a .pep suffix. These will replace the tbl2asn-generated
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conceptual translations, and can be used to verify correct CDS intervals.
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The nucleotide sequence products of mRNA features can be provided as FASTA
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files with a .rna suffix. Sequence quality scores can be supplied in files
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tbl2asn generates a .sqn file for submission to the database from these
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COMMAND-LINE ARGUMENTS
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To process a set of chromosomes, sets of .fsa and .tbl files (along with
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optional .pep, .rna, and .qvl files) are placed into a source directory.
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The path to this directory is specified in the -p command-line argument.
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The path for the resulting .sqn submission files is given in the -r
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argument. If the -r argument is not given, the .sqn files are saved in the
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For example, if an organism has fifteen chromosomes, one would expect at
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least the following files in the source directory:
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The exact names of the files are not important, but when a file with a
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suffix of .fsa is found, tbl2asn will look for a file with the same prefix
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that has a .tbl suffix, and then generate a .sqn file.
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The -t command-line argument specifies the template file.
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Normally a single FASTA sequence per .fsa file is expected. If there are
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multiple sequences, only the first is processed, unless one of two other
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flags is given. These are discussed below.
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The -s flag tells tbl2asn to package the multiple FASTA components as a set
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of unrelated sequences. This accommodates users who create a single file
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instead of one file per sequence.
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The -d flag tells the program to make a delta sequence out of the multiple
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components.This can be used for HTGS submissions where the sequence of the
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BAC/PAC clone has not been completely determined. Gaps of 100 base pairs
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should be inserted in between the actual sequence segments with lines
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containing an angle bracket '>', a question mark '?', and the length of
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The -g flag causes tbl2asn to generate a genomic product set. Within the
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set, the products of each related mRNA and CDS are packaged together in an
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internal nuc-prot set. The feature table must provide reciprocal
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protein_id and transcript_id qualifiers in order to correctly identify each
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mRNA/CDS pair. From the resulting .sqn file, the genomic sequence, all
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transcripts, and all proteins will be entered into the database and given
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accessions. Note, however, that -g cannot be used for records submitted to
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GenBank. It is only suitable for records going into RefSeq.
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If a feature table is not given, the -c flag tells tbl2asn to annotate the
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longest Open Reading Frame (ORF) on each record. The -m flag allows
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alternative start codons to be used when finding the ORF. The protein will
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be named 'unknown' unless the name is present in the .fsa file definition
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line, e.g., [protein=helicase].
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Data records will be validated when the -v flag is indicated. Output is
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saved to files with a .val suffix. The validator checks for many things,
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including internal stops in CDS features and mismatches between the CDS
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translation and the supplied protein sequence. Errors need to be corrected
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before submitting files to GenBank.
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GenBank format output is generated when the -b flag is used. Resulting
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files have a .gbf suffix.
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NUCLEOTIDE SEQUENCE FORMAT
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tbl2asn can read nucleotide sequences of any size in FASTA format. A FASTA
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record consists of a single definition line, beginning with a '>' and
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followed by optional text, and subsequent lines of sequence. At minimum,
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all definition lines must contain an identifier for the sequence, called
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the SeqID. The SeqID cannot begin with "contig", as this is reserved for
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entry of accession lists in Sequin. Other optional information about the
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biological source of the organism can also be encoded in brackets on the
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definition line. A sample definition line is
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>Sc_16 [organism=Saccharomyces cerevisiae] [strain=S288C] [chromosome=XVI]
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Other elements include [topology=circular] and [location=mitochondrion].
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Rna viruses would be indicated by [molecule=rna] and [moltype=genomic]. The
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sequencing technique can be supplied as [tech=fli cDNA]. Many other source
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qualifiers, such as map, clone, isolate, cell-line, and cultivar, can be
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used. For organisms that are not commonly submitted with tbl2asn, the
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nuclear and mitochondrial genetic codes can be indicated by [gcode=1] and
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[mgcode=3], respectively. This will ensure proper translation of CDS
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features. Primary accessions of TPA (third party annotation) records are
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given by [primary=xxx,xxx,...]. Finally, a general note can be added with
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Note that the definition line must be a single line, with no return or
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newline characters. Some word-processors will word-wrap text, either during
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display or when saving to a file, and care must be taken to avoid unwanted
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newlines introduced by the editor.
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>slpy [organism=Zea mays] [chromosome=9] Sleepy transposon
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TGTAAGATCACTGCTGGGTTGTTGATGAGTTGAGCACCGCTCCCGGCACCCGTCTCCTCTCACGAAGATC
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TTTAGGGTATGAAAAGTATCTGGAGTTCTTACACGACGGCGAGCCGCCTCTTCTCCGGACGCAGCCGGCC
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AGCCTTCTTCTCCAAGTCACCTTTTACCGACTCCAAACCCCACCTCAAATACTCCACTCAATCCAGATCA
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Multiple SeqIDs can be indicated in FASTA parsable strings.
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>gnl|ZGP|chr1|gb|U28041
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>gi|54465|emb|X16935|MMTCRAC
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tbl2asn reads features from a simple five-column tab-delimited table. This
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is described in more detail at
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http://www.ncbi.nlm.nih.gov/Sequin/table.html
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The feature table specifies the location and type of each feature, and
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tbl2asn processes the feature intervals and translates any CDSs into
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proteins. The first line of the table contains the following basic
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>Features SeqId table_name
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The SeqId must be the same as that used on the sequence. The table name is
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optional. Subsequent lines of the table list the features. Columns are
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The first and second columns are the start and stop locations of the
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feature, respectively, the third column is the type of feature (the feature
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key, e.g., gene, mRNA, CDS), the fourth column is a qualifier name (e.g.,
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"product", and the fifth is a qualifier value (e.g., the name of the protein
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A simple feature table is
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product RNA helicase SDE3
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product RNA helicase SDE3
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If a feature contains multiple intervals, each interval is listed on a
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separate line by its start and stop position. Features that are on the
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complementary strand are indicated by reversing the interval locations.
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Locations of partial (incomplete) features are indicated with a '>' or '<'
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Gene features are always a single interval, and their location should cover
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the intervals of all the relevant features. If the gene feature spans the
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intervals of the CDS or mRNA features for that gene, there is no need to
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include gene qualifiers on those features in the table, since they will be
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picked up by overlap. Use of the overlapping gene can be suppressed by
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adding a gene qualifier with the value "-". This is important when, for
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example, a tRNA is encoded within an intron of a housekeeping gene.
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Translation exception qualifiers are parsed from the same style used in the
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transl_except (pos:591..593,aa:Sec)
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The codon recognized and anticodon position of tRNAs can also be given.
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anticodon (pos:7591..7593,aa:Trp)
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In addition to the standard qualifiers seen in GenBank format, several other
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tokens are used to direct values to specific fields in the ASN.1 data.
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These include gene_syn, gene_desc, locus_tag, prot_desc, prot_note,
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region_name, bond_type, and site_type.
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Genomic product sets require protein_id and transcript_id qualifiers on each
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mRNA and CDS feature. These are used to associate the correct pair of
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features for packaging.
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transcript_id lcl|sde3m
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Exceptional biological situations can be annotated by use of the exception
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qualifier. For example
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exception ribosomal slippage
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The following are legal exception qualifier values
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reasons given in citation
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alternative processing
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artificial frameshift
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nonconsensus splice site
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rearrangement required for product
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modified codon recognition
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alternative start codon
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Since the International Nucleotide Sequence Database collaboration only
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allows "RNA editing" and "reasons given in citation" to appear in release
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mode, other exceptions are mapped to the /note qualifier in the flatfile.
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However, each exception text string turns off specific validator tests that
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would otherwise produce warning messages, so they should be entered as
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exception qualifiers.
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Gene Ontology (GO) terms can be indicated with the following qualifiers
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go_component endoplasmic reticulum|0005783
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go_process glycolysis and gluconeogenesis|57|89197757|ACT,TEM
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go_function excision repair|93||IPD
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The value field is separated by vertical bars '|' into a descriptive
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string, the GO identifier (leading zeroes are retained), and optionally a
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PubMed ID and one or more evidence codes.
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PROTEIN SEQUENCE FORMAT
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Protein sequences are FASTA files with a .pep extension that can substitute
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for the translated product of a CDS feature. Supplying these files acts as
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a reality check that the CDS intervals do in fact translate to the expected
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protein sequence. The FASTA defline with a '>' and sequence identifier are
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required, but the [gene] and [protein] data (which are used by Sequin) are
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>sde3p [gene=SDE3] [protein=RNA helicase SDE3]
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MSVSUYKSDDEYSVIADKGEIGFIDYQNDGSSGCYNPFDEGPVVVSVPFPFKKEKPQSVTVGETSFDSFT
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VKNTMDEPVDLWTKIYASNPEDSFTLSILKPPSKDSDLKERQCFYETFTLEDRMLEPGDTLTIWVSCKPK
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The SeqID must match that a protein_id in the .tbl file. In the example
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above, the protein_id and transcript_id needed to explicitly use a 'lcl|'
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prefix before the SeqID string to indicate a local identifier. A local
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sequence identifier is assumed when reading FASTA, but a database accession
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is assumed in the feature table.
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Sequin's Suggest Interval functionality, which can derive CDS intervals
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from nucleotide and protein sequences plus the genetic code, is not used in
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tbl2asn. Instead, the CDS is required, and the supplied protein sequence
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is just used to confirm proper translation.
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MESSENGER RNA SEQUENCE FORMAT
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mRNA sequences are FASTA files with a .rna extension that can substitute
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for the transcribed product of an mRNA feature. Like the .pep files, they
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act as a reality check that the supplied intervals do in fact encode the
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expected mRNA sequence.
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>sde3m [product=RNA helicase SDE3]
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TTTTCATGTTTCTTCTCCTTTGAAGCCTGCCTGCGTTAGTCTGGCTTCATTGCTTCTCCATTTCTTGGTG
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TGATCGAATCAAAGAGTGTAACCCATTTTGCTACTGATTCAGTACGTATGATCAATTCTCTCAATTTCAG
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The SeqID must match the transcript_id from an mRNA feature.
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QUALITY SCORES FORMAT
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Phrap/Consed quality scores can be supplied in .qvl files. These generate
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Seq-graph data that will be attached to the nucleotide sequence from the
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.fsa file. Programs such as Sequin can display these in a graphical view.
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51 63 70 82 82 82 90 90 90 90 86 86 86 86 90 90 90 90 90 86
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86 86 86 86 86 86 86 90 90 90 90 90 90 86 86 78 78 90 90 86
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These values can be extracted from the output files of the Phrap and Consed
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programs used to process raw data from automated sequencing machines.
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SUBMISSION TEMPLATE FORMAT
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The submission template is an ASN.1 Submit-block that can be generated by
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Sequin. A simple example is shown below.
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affil "Oxbridge University" ,
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div "Evolutionary Biology Department" ,
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country "United Kingdom" ,
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street "1859 Tennis Court Lane" ,
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email "darwin@beagle.edu.uk" ,
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phone "01 44 171-007-1212" ,
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postal-code "OX1 2BH" } } } ,
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initials "C.R." } } } ,
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affil "Oxbridge University" ,
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div "Evolutionary Biology Department" ,
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country "United Kingdom" ,
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street "1859 Tennis Court Lane" ,
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postal-code "OX1 2BH" } } ,
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This can be exported from the Desktop view of a template file in Sequin. In
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addition, unpublished reference or comments can also be generated in Sequin
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and saved from the Desktop. The two files can be catenated to make a .sbt
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template with the publication or comment descriptor after the submit block.
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doc/tbl2asn.txt
