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TBL2ASN(1) NCBI Tools User's Manual TBL2ASN(1)


tbl2asn - prepare a GenBank submission using an ASCII feature table


tbl2asn [-] [-A str] [-C str] [-D filename] [-E] [-F str] [-G str] [-H str] [-J] [-K] [-L] [-M str] [-N n] [-O] [-P] [-Q str] [-R] [-S] [-T] [-U] [-V str] [-W] [-X str] [-Y filename] [-Z filename] [-a str] [-b] [-c str] [-f filename] [-g] [-h] [-i filename] [-j str] [-k str] [-l str] [-m str] [-n str] [-o filename] [-p str] [-q] [-r str] [-s] [-t filename] [-u] [-v] [-w filename] [-x str] [-y str] [-z]


tbl2asn reads a template along with sequence and table files, and outputs ASN.1 for submission to GenBank. Thus, the submitter does not need to read each set of table and sequence files into Sequin. Furthermore, the template file can contain the organism and submitter information common to all records, obviating the need to input these data for each sequence/table pair.


A summary of options is included below.

Print usage message
-a str
-C str
Genome Center tag
-D filename
Descriptors file
Feature ID links:
By Overlap
By Product
By Label and Location
Suppress links forced by -M
Alignment Gap Flags (comma separated fields, e.g., p,-,-,-,?,. ) n Nucleotide or p Protein, Begin, Middle, End Gap Characters, Missing Characters, Match Characters Alignment middle Gap characters
Hold until publication:
For one year
Until the specified date
Delayed genomic product set
Safe Bioseq-set
Force Local protein_id/transcript_id
Master genome flags:
Big sequence
Power option
Project version number
Allow run-on ORFs
Remote publication lookup
mRNA title policy
Special mRNA titles
RefSeq mRNA titles
Remote sequence record fetching from ID
Smart feature annotation
Remote Taxonomy lookup
Remove Unnecessary gene xref
Verification (combine any of the following letters)
Validate with Normal Stringency
Validate without Country Check
BarCode validation
Generate GenBank Flatfile
Generate Gene Report
Validate with TSA check
Log progress
Extra flags (combine any of the following letters)
Automatic definition line generation
Apply Comments in .cmt files to all sequences
Treat like Eukarypota in the discrepancy report
Read a comment string from filename
Write a discrepancy report to filename
-a str
File type:
Any (default)
Runs of 20+ Ns are gaps, 100 Ns are unknown length
Runs of 20+ Ns are gaps, 100 Ns are known length
Runs of 10+ Ns are gaps, 100 Ns are unknown length
Runs of 10+ Ns are gaps, 100 Ns are known length
FASTA Set (s Batch, s1 Pop, s2 Phy, s3 Mut, s4 Eco, s9 Small-genome)
FASTA Delta with Implicit Gaps
FASTA+Gap Alignment (l Batch, l1 Pop, l2 Phy, l3 Mut, l4 Eco, l9 Small-genome)
FASTA with Gap Lines
ASN.1 (in conjunction with
Generate GenBank file (deprecated in favor of -V b)
-c str
Cleanup (combine any of the following letters)
Correct Collection Dates (assume month first)
Correct Collection Dates (assume day first)
Append note to coding regions that overlap other coding regions with similar product names and do not contain 'ABC'
Extend partial ends of features by one or two nucleotides to abut gaps or sequence ends
Add exception to non-extendable partials
Add exception to short introns
Fix product names
-f filename
Single table file
Input is a genomic product set
Convert general ID to note
Single input file
Source qualifiers
-k str
CDS flags (combine any of the following letters)
Annotate Longest ORF
Allow Runon ORFs
Allow Alternative Starts
Set Conflict on Mismatch
-l str
Add type of evidence used to assert linkage across assembly gaps (only for TSA records). Must be one of the following:
-m str
Lineage to use for discrepancy report tests
-n str
Organism name
-o filename
Single output file
-p str
Path to files
Set sequence ID from input file name
-r str
Path for results
Read FASTAs as Set
-t filename
Read template from filename
Convert GenProdSet to NucProtSet
Validate (deprecated in favor of -V v)
Single structured comment file (overrides the use of -X C)
-x str
Suffix (default = .fsa)
-y str
Clean up log file Comment


The National Center for Biotechnology Information.


Psequin(1), sbtedit(1), /usr/share/doc/ncbi-tools-bin/tbl2asn.txt.gz, <>.

2016-09-01 NCBI