NCBI C Toolkit Cross Reference

   TBL2ASN AUTOMATED BULK SUBMISSION PROGRAM
   
   tbl2asn is a program that automates the submission of sequence records to
   GenBank.  It uses many of the same functions as Sequin, but is driven
   entirely by data files, and records need no additional manual editing before
   submission.  Entire genomes, consisting of many chromosomes with feature
   annotation, can be processed in seconds using this method.
   
   For a submission, tbl2asn expects a template file containing a text ASN.1
  Submit-block object.  These can be generated in Sequin and saved for use by
  tbl2asn.  The Submit-block contains contact information (to whom questions
  on the submission can be addressed) and a submission citation (which lists
  the authors who get scientific credit for the sequencing).
  
  The template file can also contain one or more text ASN.1 Seq-descr objects
  (such as Title or BioSource) appended after the Submit-block.  These can
  also be generated in Sequin and saved to a file, and then appended to the
  template with a text editor.  They will become descriptors packaged at the
  top of each submission file.
  
  tbl2asn reads six other kinds of data files.  Nucleotide sequence data is
  expected in FASTA format, and these files are identified by having a .fsa
  suffix.  Feature table files, in the five-column format described later,
  have a .tbl suffix.  These can be easily generated by most genome centers
  that maintain feature locations in a spreadsheet or database.  For sets of
  data records, a source qualifier table can be placed in a .src file.  The
  protein translations of CDS features can be supplied as FASTA sequences in
  files with a .pep suffix.  These will replace the tbl2asn-generated
  conceptual translations, and can be used to verify correct CDS intervals.
  The nucleotide sequence products of mRNA features can be provided as FASTA
  files with a .rna suffix.  Sequence quality scores can be supplied in files
  with a .qvl suffix.
  
  tbl2asn generates a .sqn file for submission to the database from these
  input files.
  
  
  COMMAND-LINE ARGUMENTS
  
  To process a set of chromosomes, sets of .fsa and .tbl files (along with
  optional .src, .pep, .rna, and .qvl files) are placed into a source
  directory.  The path to this directory is specified in the -p command-line
  argument.  The path for the resulting .sqn submission files is given in the
  -r argument.  If the -r argument is not given, the .sqn files are saved in
  the source directory.
  
  For example, if an organism has fifteen chromosomes, one would expect at
  least the following files in the source directory:
  
    chr01.fsa
    chr01.tbl
    chr02.fsa
    ...
    chr14.tbl
    chr15.fsa
    chr15.tbl
  
  The exact names of the files are not important, but when a file with a
  suffix of .fsa is found, tbl2asn will look for a file with the same prefix
  that has a .tbl suffix, and then generate a .sqn file.
  
  The -t command-line argument specifies the template file.
  
  Normally a single FASTA sequence per .fsa file is expected.  If there are
  multiple sequences, only the first is processed, unless one of two -a flag
  variants are given.  These are discussed below.
  
  The -a s flag tells tbl2asn to package the multiple FASTA components as a set
  of unrelated sequences.  This accommodates users who create a single file
  instead of one file per sequence.  A single FASTA component can now have gap
  indications (e.g., >?unk100) on a separate line as long as it is followed
  immediately by more sequence lines, with no > and a mock identifier.
  
  The -a d flag tells the program to make a delta sequence out of the multiple
  components.  This can be used for HTGS submissions where the sequence of
  the BAC/PAC clone has not been completely determined.  By convention, gaps
  of 100 base pairs should be inserted in between the actual sequence
  segments with lines containing an angle bracket '>', a question mark '?',
  the letters "unk", and the length of the gap.
  
  >?unk100
  
  The -g flag causes tbl2asn to generate a genomic product set.  Within the
  set, the products of each related mRNA and CDS are packaged together in an
  internal nuc-prot set.  The feature table must provide reciprocal
  protein_id and transcript_id qualifiers in order to correctly identify each
  mRNA/CDS pair.  From the resulting .sqn file, the genomic sequence, all
  transcripts, and all proteins will be entered into the database and given
  accessions.  Note, however, that -g cannot be used for records submitted to
  GenBank.  It is only suitable for records going into RefSeq.
  
  If a feature table is not given, the -k c flag tells tbl2asn to annotate the
  longest Open Reading Frame (ORF) on each record.  The -k m flag allows
  alternative start codons to be used when finding the ORF.  The protein will
  be named 'unknown' unless the name is present in the .fsa file definition
  line, e.g., [protein=helicase].  The two flags can be combined as -k cm.
  
  Data records will be validated when the -V v flag is indicated.  Output is
  saved to files with a .val suffix.  The validator checks for many things,
 including internal stops in CDS features and mismatches between the CDS
 translation and the supplied protein sequence.  Errors need to be corrected
 before submitting files to GenBank.
 
 GenBank format output is generated when the -V b flag is used.  Resulting
 files have a .gbf suffix.  The validation and flatfile generation flags can
 be combined as -V vb.
 
 
 NUCLEOTIDE SEQUENCE FORMAT
 
 tbl2asn can read nucleotide sequences of any size in FASTA format.  A FASTA
 record consists of a single definition line, beginning with a '>' and
 followed by optional text, and subsequent lines of sequence.  At minimum,
 all definition lines must contain an identifier for the sequence, called
 the SeqID.  The SeqID cannot begin with "assembly", as this is reserved for
 entry of accession lists in Sequin.  Other optional information about the
 biological source of the organism can also be encoded in brackets on the
 definition line.  A sample definition line is
 
 >Sc_16 [organism=Saccharomyces cerevisiae] [strain=S288C] [chromosome=XVI]
 
 Other elements include [topology=circular] and [location=mitochondrion].
 Rna viruses would be indicated by [molecule=rna] and [moltype=genomic]. The
 sequencing technique can be supplied as [tech=fli cDNA].  Many other source
 qualifiers, such as map, clone, isolate, cell-line, and cultivar, can be
 used.  For organisms that are not commonly submitted with tbl2asn, the
 nuclear and mitochondrial genetic codes can be indicated by [gcode=1] and
 [mgcode=3], respectively.  This will ensure proper translation of CDS
 features.  Primary accessions of TPA (third party annotation) records are
 given by [primary=xxx,xxx,...].  Finally, a general note can be added with
 [note=xxx].
 
 Note that the definition line must be a single line, with no return or
 newline characters.  Some word-processors will word-wrap text, either during
 display or when saving to a file, and care must be taken to avoid unwanted
 newlines introduced by the editor.
 
 >slpy [organism=Zea mays] [chromosome=9] Sleepy transposon
 TGTAAGATCACTGCTGGGTTGTTGATGAGTTGAGCACCGCTCCCGGCACCCGTCTCCTCTCACGAAGATC
 TTTAGGGTATGAAAAGTATCTGGAGTTCTTACACGACGGCGAGCCGCCTCTTCTCCGGACGCAGCCGGCC
 AGCCTTCTTCTCCAAGTCACCTTTTACCGACTCCAAACCCCACCTCAAATACTCCACTCAATCCAGATCA
 ...
 
 Multiple SeqIDs can be indicated in FASTA-style parsable strings.
 
 >gnl|ZGP|chr1|gb|U28041
 >gi|54465|emb|X16935|MMTCRAC
 
 
 FEATURE TABLE FORMAT
 
 tbl2asn reads features from a simple five-column tab-delimited table.  This
 is described in more detail at
 
 http://www.ncbi.nlm.nih.gov/Sequin/table.html
 
 The feature table specifies the location and type of each feature, and
 tbl2asn processes the feature intervals and translates any CDSs into
 proteins. The first line of the table contains the following basic
 information.
 
 >Feature SeqId table_name 
 
 The SeqId must be the same as that used on the sequence. The table name is
 optional.  Subsequent lines of the table list the features.  Columns are
 separated by tabs.
 
 The first and second columns are the start and stop locations of the
 feature, respectively, the third column is the type of feature (the feature
 key, e.g., gene, mRNA, CDS), the fourth column is a qualifier name (e.g.,
 "product", and the fifth is a qualifier value (e.g., the name of the protein
 or gene).
 
 A simple feature table is
 
 >Feature sde3g
 240     4084    gene
                         gene    SDE3
 240     1361    mRNA
 1450    1641
 1730    3184
 3275    4084
                         product RNA helicase SDE3
 
 579     1361    CDS
 1450    1641
 1730    3184
 3275    3880
                         product RNA helicase SDE3
 
 If a feature contains multiple intervals, each interval is listed on a
 separate line by its start and stop position.   Features that are on the
 complementary strand are indicated by reversing the interval locations. 
 Locations of partial (incomplete) features are indicated with a '>' or '<'
 next to the number.
 
 Gene features are always a single interval, and their location should cover
 the intervals of all the relevant features.  If the gene feature spans the
 intervals of the CDS or mRNA features for that gene, there is no need to
 include gene qualifiers on those features in the table, since they will be
 picked up by overlap.  Use of the overlapping gene can be suppressed by
 adding a gene qualifier with the value "-".  This is important when, for
 example, a tRNA is encoded within an intron of a housekeeping gene.
 
 Translation exception qualifiers are parsed from the same style used in the
 GenBank flatfile.
 
                         transl_except   (pos:591..593,aa:Sec)
 
 The codon recognized and anticodon position of tRNAs can also be given.
 
                         codon_recognized   TGG
                         anticodon   (pos:7591..7593,aa:Trp)
 
 In addition to the standard qualifiers seen in GenBank format, several other
 tokens are used to direct values to specific fields in the ASN.1 data. 
 These include gene_syn, gene_desc, locus_tag, prot_desc, prot_note,
 region_name, bond_type, and site_type.
 
 Genomic product sets require protein_id and transcript_id qualifiers on each
 mRNA and CDS feature.  These are used to associate the correct pair of
 features for packaging.
 
                         protein_id      lcl|sde3p
                         transcript_id   lcl|sde3m
 
 Exceptional biological situations can be annotated by use of the exception
 qualifier.  For example
 
                         exception       ribosomal slippage
 
 The following are legal exception qualifier values
 
   RNA editing
   reasons given in citation
   ribosomal slippage
   trans-splicing
   alternative processing
   artificial frameshift
   nonconsensus splice site
   rearrangement required for product
   modified codon recognition
   alternative start codon
   dicistronic gene
   transcribed pseudogene
 
 Since the International Nucleotide Sequence Database collaboration only
 allows "RNA editing" and "reasons given in citation" to appear in release
 mode, other exceptions are mapped to the /note qualifier in the flatfile.
 However, each exception text string turns off specific validator tests that
 would otherwise produce warning messages, so they should be entered as
 exception qualifiers, not as notes.
 
 Gene Ontology (GO) terms can be indicated with the following qualifiers
 
                         go_component    endoplasmic reticulum|0005783
                         go_process      glycolysis and gluconeogenesis|57|89197757|ACT,TEM
                         go_function     excision repair|93||IPD
 
 The value field is separated by vertical bars '|' into a descriptive
 string, the GO identifier (leading zeroes are retained), and optionally a
 PubMed ID (or GO Reference number starting with a leading 0) and one or more
 GO evidence codes.
 
 
 SOURCE TABLE FORMAT
 
 For sets of sequences, a source qualifier table can optionally be placed in
 a tab-delimited file with a .src extension.  The first line gives the
 source qualifier names, separated by tabs.  The first column must be the
 sequence identifier.  For example
 
 sequence_id     organism    strain       isolate
 
 The remaining lines each give the source qualifiers for one sequence.  For
 example
 
 sde3g           Zea mays    A69Y         JH90.6-2x12
 
 The same information can be provided in the FASTA definition line or in the
 source section of the five-column feature table.
 
 
 PROTEIN SEQUENCE FORMAT
 
 Protein sequences are FASTA files with a .pep extension that can substitute
 for the translated product of a CDS feature.  Supplying these files acts as
 a reality check that the CDS intervals do in fact translate to the expected
 protein sequence.  The FASTA defline with a '>' and sequence identifier is
 required.
 
 >sde3p
 MSVSUYKSDDEYSVIADKGEIGFIDYQNDGSSGCYNPFDEGPVVVSVPFPFKKEKPQSVTVGETSFDSFT
 VKNTMDEPVDLWTKIYASNPEDSFTLSILKPPSKDSDLKERQCFYETFTLEDRMLEPGDTLTIWVSCKPK
 ...
 
 The SeqID must match a protein_id in the .tbl file.  In the table above,
 the protein_id and transcript_id need to explicitly use a 'lcl|' prefix
 before the SeqID string to indicate a local identifier.  A local sequence
 identifier is assumed when reading FASTA, but a database accession is
 assumed in the feature table.
 
 Sequin's Suggest Interval functionality, which can determine CDS intervals
 from nucleotide and protein sequences plus the genetic code, is not used in
 tbl2asn.  Instead, the CDS intervals are required, and the supplied protein
 sequence is just used to confirm proper translation.
 
 
 MESSENGER RNA SEQUENCE FORMAT
 
 mRNA sequences are FASTA files with a .rna extension that can substitute
 for the transcribed product of an mRNA feature.  Like the .pep files, they
 act as a reality check that the supplied intervals do in fact encode the
 expected mRNA sequence.
 
 >sde3m
 TTTTCATGTTTCTTCTCCTTTGAAGCCTGCCTGCGTTAGTCTGGCTTCATTGCTTCTCCATTTCTTGGTG
 TGATCGAATCAAAGAGTGTAACCCATTTTGCTACTGATTCAGTACGTATGATCAATTCTCTCAATTTCAG
 ...
 
 The SeqID must match the transcript_id from an mRNA feature.
 
 
 QUALITY SCORES FORMAT
 
 Phrap/Consed quality scores can be supplied in .qvl files.  These generate
 Seq-graph data that will be attached to the nucleotide sequence from the
 .fsa file. Programs such as Sequin can display these in a graphical view.
 
 >chr1
  51 63 70 82 82 82 90 90 90 90 86 86 86 86 90 90 90 90 90 86
  86 86 86 86 86 86 86 90 90 90 90 90 90 86 86 78 78 90 90 86
 ...
 
 These values can be extracted from the output files of the Phrap and Consed
 programs used to process raw data from automated sequencing machines.
 
 
 SUBMISSION TEMPLATE FORMAT
 
 The submission template is an ASN.1 Submit-block that can be generated by
 Sequin.  A simple example is shown below.
 
 Submit-block ::= {
   contact {
     contact {
       name
         name {
           last "Darwin" ,
           first "Charles" ,
           initials "C.R." ,
           suffix "" } ,
       affil
         std {
           affil "Oxbridge University" ,
           div "Evolutionary Biology Department" ,
           city "Camford" ,
           country "United Kingdom" ,
           street "1859 Tennis Court Lane" ,
           email "darwin@beagle.edu.uk" ,
           phone "01 44 171-007-1212" ,
           postal-code "OX1 2BH" } } } ,
   cit {
     authors {
       names
         std {
           {
             name
               name {
                 last "Darwin" ,
                 first "Charles" ,
                 initials "C.R." } } } ,
       affil
         std {
           affil "Oxbridge University" ,
           div "Evolutionary Biology Department" ,
           city "Camford" ,
           country "United Kingdom" ,
           street "1859 Tennis Court Lane" ,
           postal-code "OX1 2BH" } } ,
     date
       std {
         year 2003 ,
         month 2 ,
         day 28 } } ,
   subtype new  }
 
 This can be exported from the Desktop view of a template file in Sequin, or
 from the initial submission dialogs.  In addition, unpublished reference or
 comments can also be generated in Sequin and saved from the Desktop.  The
 two files can be catenated to make a .sbt template with the publication or
 comment descriptor after the submit block.