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Man Pages


Manual Reference Pages  -  TBL2ASN (1)

NAME

tbl2asn - prepare a GenBank submission using an ASCII feature table

CONTENTS

Synopsis
Description
Options
Author
See Also

SYNOPSIS

tbl2asn [-] [-A str] [-C str] [-D filename] [-E] [-F str] [-G str] [-H str] [-K] [-L] [-O] [-P] [-Q] [-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] [-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 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)
-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 characters
-H str Hold until publication:
y For one year
mm/dd/yyyy Until the specified date
-K Safe Bioseq-set
-L Force Local protein_id/transcript_id
-O Allow run-on ORFs
-P Remote publication lookup
-Q Special 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
b Generate GenBank Flatfile
g Generate Gene Report
-W Log progress
-X str Extra flags (combine any of the following letters)
C Apply comments in .cmt files to all sequences
-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
s FASTA Set (s Batch, s1 Pop, s2 Phy, s3 Mut, s4 Eco)
d FASTA Delta
di FASTA Delta with Implicit Gaps
l FASTA+Gap Alignment
z FASTA with Gap Lines
e PHRAP/ACE
-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
-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)
-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/Sequin/table.html>.
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NCBI TBL2ASN (1) 2009-07-31

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