tbl2asn − prepare a GenBank submission using an ASCII feature table
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]
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.
A summary of options is included below.
− |
Print usage message |
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−a str |
Accession |
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−C str |
Genome Center tag |
−D filename
Descriptors file
−F |
Feature ID links (o by Overlap, p by Product) |
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−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 |
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−H |
Implicit gaps (deprecated in favor of -a di) |
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−K |
Safe Bioseq-set |
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−L |
Force Local protein_id/transcript_id |
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−O |
Allow run-on ORFs |
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−P |
Remote publication lookup |
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−Q |
Special mRNA titles |
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−R |
Remote sequence record fetching from ID |
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−S |
Smart feature annotation |
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−T |
Remote Taxonomy lookup |
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−U |
Remove Unnecessary gene xref |
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−V str |
Verification (combine any of the following letters) |
v
Validate with Normal Stringency |
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r |
Validate without Country Check |
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b |
Generate GenBank Flatfile |
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−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) |
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r20u |
Runs of 20+ Ns are gaps, 100 Ns are unknown length |
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r20k |
Runs of 20+ Ns are gaps, 100 Ns are known length |
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s |
FASTA Set (s Batch, s1 Pop, s2 Phy, s3 Mut, s4 Eco) |
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d |
FASTA Delta |
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di |
FASTA Delta with Implicit Gaps |
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l |
FASTA+Gap Alignment |
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z |
FASTA with Gap Lines |
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e |
PHRAP/ACE |
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−b |
Generate GenBank file (deprecated in favor of -V b)
−c |
Annotate longest ORF (deprecated in favor of -k c) |
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−d |
Read FASTAs as Delta (deprecated in favor of -a d) |
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−e |
Read PHRAP/ACE format (deprecated in favor of -a e) |
−f filename
Single table file
−g |
Input is a genomic product set |
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−h |
Convert general ID to note |
−i filename
Single input file
−j str |
Source qualifiers |
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−k str |
CDS flags (combine any of the following letters) |
c
Annotate Longest ORF |
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r |
Allow Runon ORFs |
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m |
Allow Alternative Starts |
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k |
Set Conflict on Mismatch |
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−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 |
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−q |
Set sequence ID from input file name |
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−r str |
Path for results |
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−s |
Read FASTAs as Set |
−t filename
Read template from filename
−u |
Convert GenProdSet to NucProtSet |
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−v |
Validate (deprecated in favor of -V v) |
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−w N |
FASTA set class (deprecated in favor of -a sN) |
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−x str |
Suffix (default = .fsa) |
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−y str |
Comment |
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−z |
Read FASTAs with gap lines (deprecated in favor of -a z) |
The National Center for Biotechnology Information.
Psequin(1), sbtedit(1), /usr/share/doc/ncbi-tools-bin/tbl2asn.txt.gz, <http://www.ncbi.nlm.nih.gov/Sequin/table.html>.