man tbl2asn (Commandes) - prepare a GenBank submission using an ASCII feature table
NAME
tbl2asn - prepare a GenBank submission using an ASCII feature table
SYNOPSIS
tbl2asn [-] [-B str] [-C str] [-E str] [-G str] [-L] [-M str] [-P] [-Q] [-R] [-S] [-T] [-U] [-X str] [-Y filename] [-a str] [-b] [-c] [-d] [-e] [-g] [-h] [-i filename] [-j str] [-k] [-l] [-m] [-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
- -B str
- Alignment Beginning gap characters
- -C str
- Genome Center tag
- -E str
- Alignment End gap characters
- -G str
- Alignment middle Gap characters
- -L
- Force Local protein_id/transcript_id
- -M str
- Alignment Match characters
- -P
- Alignment is Proteins
- -Q
- Special mRNA titles
- -R
- Remote fetching from ID
- -S
- Smart feature annotation
- -T
- Remote Taxonomy lookup
- -U
- Remove Unnecessary gene xref
- -X str
- Alignment missing characters
- -Y filename
- Read a comment string from filename
- -a str
- Accession
- -b
- Generate GenBank file
- -c
- Annotate longest ORF
- -d
- Read FASTAs as Delta
- -e
- Read PHRAP/ACE format
- -g
- Input is a genomic product set
- -h
- Convert general ID to note
- -i filename
- Single input file
- -j str
- Source qualifiers
- -k
- Set conflict on mismatch
- -l
- Read FASTA+Gap Alignment
- -m
- Allow alternative starts
- -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
- -w N
- FASTA set class
- 0
- unspecified (default)
- 1
- population study
- 2
- phylogenetic study
- 3
- set of mutations
- 4
- ecological sample study
- -x str
- Suffix (default = .fsa)
- -y str
- Comment
- -z
- Read FASTAs with gap lines
AUTHOR
The National Center for Biotechnology Information.