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

NAME
       tbl2asn - prepare a GenBank submission using an ASCII feature table

SYNOPSIS
       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]

DESCRIPTION
       tbl2asn reads a template	along with sequence and	table files, and  out-
       puts 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.

OPTIONS
       A summary of options is included	below.

       -      Print usage message

       -a str Accession

       -C str Genome Center tag

       -D filename
	      Descriptors file

       -E     Recurse

       -F     Feature ID links:
	      o	     By	Overlap
	      p	     By	Product
	      l	     By	Label and Location
	      s	     Suppress links forced by -M

       -G str 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 char-
	      acters

       -H str Hold until publication:
	      y	     For one year
	      mm/dd/yyyy
		     Until the specified date

       -J     Delayed genomic product set

       -K     Safe Bioseq-set

       -L     Force Local protein_id/transcript_id

       -M str Master genome flags:
	      n	     Normal
	      b	     Big sequence
	      p	     Power option
	      t	     TSA

       -N n   Project version number

       -O     Allow run-on ORFs

       -P     Remote publication lookup

       -Q     mRNA title policy
	      s	     Special mRNA titles
	      r	     RefSeq mRNA titles

       -R     Remote sequence record fetching from ID

       -S     Smart feature annotation

       -T     Remote Taxonomy lookup

       -U     Remove Unnecessary gene xref

       -V str Verification (combine any	of the following letters)
	      v	     Validate with Normal Stringency
	      r	     Validate without Country Check
	      c	     BarCode validation
	      b	     Generate GenBank Flatfile
	      g	     Generate Gene Report
	      t	     Validate with TSA check

       -W     Log progress

       -X str Extra flags (combine any of the following	letters)
	      A	     Automatic definition line generation
	      C	     Apply Comments in .cmt files to all sequences
	      E	     Treat like	Eukarypota in the discrepancy report

       -Y filename
	      Read a comment string from filename

       -Z filename
	      Write a discrepancy report to filename

       -a str File type:
	      a	     Any (default)
	      r20u   Runs of 20+ Ns are	gaps, 100 Ns are unknown length
	      r20k   Runs of 20+ Ns are	gaps, 100 Ns are known length
	      r10u   Runs of 10+ Ns are	gaps, 100 Ns are unknown length
	      r10k   Runs of 10+ Ns are	gaps, 100 Ns are known length
	      s	     FASTA Set (s Batch, s1 Pop, s2 Phy, s3 Mut,  s4  Eco,  s9
		     Small-genome)
	      d	     FASTA Delta
	      di     FASTA Delta with Implicit Gaps
	      l	     FASTA+Gap	Alignment (l Batch, l1 Pop, l2 Phy, l3 Mut, l4
		     Eco, l9 Small-genome)
	      z	     FASTA with	Gap Lines
	      e	     PHRAP/ACE			-
	      b	     ASN.1 (in conjunction with	M
						)
       -b     Generate GenBank file (deprecated	in favor of -V b)

       -c str Cleanup (combine any of the following letters)
	      d	     Correct Collection	Dates (assume month first)
	      D	     Correct Collection	Dates (assume day first)
	      b	     Append note to coding regions that	overlap	 other	coding
		     regions  with  similar  product  names and	do not contain
		     'ABC'
	      x	     Extend partial ends of features by	one or two nucleotides
		     to	abut gaps or sequence ends
	      p	     Add exception to non-extendable partials
	      s	     Add exception to short introns
	      f	     Fix product names

       -f filename
	      Single table file

       -g     Input is a genomic product set

       -h     Convert general ID to note

       -i filename
	      Single input file

       -j str Source qualifiers

       -k str CDS flags	(combine any of	the following letters)
	      c	     Annotate Longest ORF
	      r	     Allow Runon ORFs
	      m	     Allow Alternative Starts
	      k	     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:
	      paired-ends
	      align-genus
	      align-xgenus
	      align-trnscpt
	      within-clone
	      clone-contig
	      map
	      strobe

       -m str Lineage to use for discrepancy report tests

       -n str Organism name

       -o filename
	      Single output file

       -p str Path to files

       -q     Set sequence ID from input file name

       -r str Path for results

       -s     Read FASTAs as Set

       -t filename
	      Read template from filename

       -u     Convert GenProdSet to NucProtSet

       -v     Validate (deprecated in favor of -V v)

       -w filename
	      Single structured	comment	file (overrides	the use	of -X C)

       -x str Suffix (default =	.fsa)

       -y str

       -z     Clean up log file	Comment

AUTHOR
       The National Center for Biotechnology Information.

SEE ALSO
       Psequin(1), sbtedit(1), tbl2asn.txt, <http://www.ncbi.nlm.nih.gov/Se-
       quin/table.html>.

NCBI				  2016-09-01			    TBL2ASN(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO

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