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TBL2ASN(1) NCBI Tools User's Manual TBL2ASN(1) NAME tbl2asn - prepare a GenBank submission using an ASCII feature table SYNOPSIS tbl2asn [-] [-A str] [-C str] [-D filename] [-E] [-F str] [-G str] [-H str] [-J] [-K] [-L] [-M str] [-N n] [-O] [-P] [-Q str] [-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] [-l str] [-m str] [-n str] [-o filename] [-p str] [-q] [-r str] [-s] [-t filename] [-u] [-v] [-w filename] [-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 l By Label and Location s Suppress links forced by -M -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 -J Delayed genomic product set -K Safe Bioseq-set -L Force Local protein_id/transcript_id -M str Master genome flags: n Normal b Big sequence p Power option t TSA -N n Project version number -O Allow run-on ORFs -P Remote publication lookup -Q mRNA title policy s Special mRNA titles r RefSeq 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 c BarCode validation b Generate GenBank Flatfile g Generate Gene Report t Validate with TSA check -W Log progress -X str Extra flags (combine any of the following letters) A Automatic definition line generation C Apply Comments in .cmt files to all sequences E Treat like Eukarypota in the discrepancy report -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 r10u Runs of 10+ Ns are gaps, 100 Ns are unknown length r10k Runs of 10+ Ns are gaps, 100 Ns are known length s FASTA Set (s Batch, s1 Pop, s2 Phy, s3 Mut, s4 Eco, s9 Small- genome) d FASTA Delta di FASTA Delta with Implicit Gaps l FASTA+Gap Alignment (l Batch, l1 Pop, l2 Phy, l3 Mut, l4 Eco, l9 Small-genome) z FASTA with Gap Lines e PHRAP/ACE - b ASN.1 (in conjunction with M.PD -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 re- gions 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 p Add exception to non-extendable partials s Add exception to short introns f Fix product names -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 str Add type of evidence used to assert linkage across assembly gaps (only for TSA records). Must be one of the following: paired-ends align-genus align-xgenus align-trnscpt within-clone clone-contig map strobe -m str Lineage to use for discrepancy report tests -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 filename Single structured comment file (overrides the use of -X C) -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/Se- quin/table.html>. NCBI 2016-09-01 TBL2ASN(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO
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