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tbl2asn

NAME

tbl2asn - prepare a GenBank submission using an ASCII feature table

SYNOPSIS

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

-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

Implicit gaps (deprecated in favor of -a di)

-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

-W

Log progress

-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

Annotate longest ORF (deprecated in favor of -k c)

-d

Read FASTAs as Delta (deprecated in favor of -a d)

-e

Read PHRAP/ACE format (deprecated in favor of -a e)

-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

Read FASTA+Gap Alignment (deprecated in favor of -a l)

-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 N

FASTA set class (deprecated in favor of -a sN)

-x str

Suffix (default = .fsa)

-y str

Comment

-z

Read FASTAs with gap lines (deprecated in favor of -a z)

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>.