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]
       [-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 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 infor-
       mation 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)

       -G str Alignment Gap Flags (comma separated fields, e.g., p,-,-,-,?,. ) n Nucleotide or p Protein, Begin, Middle, End Gap Characters, Miss-
	      ing Characters, Match Characters Alignment middle Gap characters

       -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
	      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

       -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

       -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), /usr/share/doc/ncbi-tools-bin/tbl2asn.txt.gz, <http://www.ncbi.nlm.nih.gov/Sequin/table.html>.

NCBI
								    2012-06-24								TBL2ASN(1)