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tbl2asn
Langue: en
Version: 335396 (ubuntu - 24/10/10)
Section: 1 (Commandes utilisateur)
NAME
tbl2asn - prepare a GenBank submission using an ASCII feature tableSYNOPSIS
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), /usr/share/doc/ncbi-tools-bin/tbl2asn.txt.gz, <http://www.ncbi.nlm.nih.gov/Sequin/table.html>.Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre