-p	Path to the directory. If files are in the current directory -p. should be used.
-r	Path for the resulting .sqn submission file (if the -r argument is not given 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.
-s	Instructs tbl2asn to read multiple FASTA components in one file as a set of unrelated sequences. This creates a single file of multiple submissions. (1000 sequences per file is the maximum.)
-c	Instructs tbl2asn to annotate the longest open reading frame (orf) if a .tbl file is not provided.
-m	Allows alternative start codons to be used in orf searches.
-v	Validates the data records. The output is saved to files with a .val suffix.
-b	Generates GenBank flatfiles with a .gbf suffix.
-i	Creates single submission from indicated .fsa file in a directory of multiple .fsa files.
-j	Allows the addition of source qualifiers that will be the same for each submission. Example: -j "[organism=Saccharomyces cerevisiae] [strain=S288C]".
-y	Adds a COMMENT to each submission. Example: -y "Contigs larger than 2kb have been annotated, representing approx. 87% of the total genome".
-o	Creates a single submission from multiple fasta files.
-l	Reads one or more FASTA+GAP alignments to create one or more phylogenetic sets.

Note: When using -c to annotate the longest orf, the product name is entered as unknown unless one is provided in the .fsa file definition line.

Note: Please review the .val files and correct any error level errors.

Examples:

tbl2asn -t template.sbt -p path_to_files -v

tbl2asn -t template.sbt -p path_to_files -s -v

tbls2asn -t template.sbt -i x.fsa -v

Nucleotide sequence and FASTA defline formats (.fsa)

• SeqID (sequence identifier) which is the text between the '>' and the first space. The SeqID cannot begin with 'contig', as this identifier is reserved for another use and will generate errors.
• Organism and related information

Biological
• strain [strain=S288C]
• isolate [isolate=CWS1]
• chromosome [chromosome=XVI]

Other elements
• topology [topology=circular]
• location [location=mitochondrion]
• molecule [moltype=RNA] (DNA is the default)
• technique [tech=wgs]
• protein name [product=helicase] (if using -c)

Click on Source and/or Organism for the complete list of modifiers.

Example FASTA:

>Sc_16 [organism=Saccharomyces cerevisiae]
tataggcgaatcgagtatattattttttctcaacatatgtat
atgaacatgagaatatatttataggaatgtataaaattgtga
cctctcctgctattttagttactgattttatgtatgtagggg
gaataggggctgcctttcttaatgcagttttaattttttctt
ttaattttttcttagtaaaattatttaaagtaaagattaatg
gaataaccattgcgcttttttttacagtttttggtttttcat
tttttggaaaaaatattttaaatattttacctttttatttag
ggggtattttatatagtatctatacttcaacagatttttctg
aacatatagttcctattgctttttcaagtgcattagcccctt
ttgtaagcagtgttgcttttatggagaaatatcctatgaaac
atcatatataaattttaattggtattttaattggttttatag
tggttcctttgtctaaaagtctttatgactttcatgagggat
atgattttatataatttaggttttacagcaggtttag

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
                        

Protein sequence format (.pep)

• Set up as a FASTA file using the protein sequence.
• This file will substitute the automatically translated products of the CDS features with the provided protein sequences.
• Serves as a check that the conceptual translation of the nucleotide sequence is as predicted.
• SeqID must match protein_id in the .tbl file

Example FASTA:

>WS1030 [gene=sde3p] [protein=SDE3P]
MYKIVTSPAILVTDFMYVGGIGAAFLNAVLIFSFNFFL
VKLFKVKINGITIAAFFTVFGFSFFGKNILNILPFYLG
GILYSIYTSTDFSEHIVPIAFSSALAPFVSSVAFYGEI
SYETSYINAILIGILIGFIVVPLSKSLYDFHEGYDLYN
LGFTAG

Quality scores table format (.qvl)

>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...

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Revised: March 12, 2004.