TBL2ASN(1)

💖 TBL2ASN(1) 💖 the NCBI Tools User's Manual, but make it a group chat

hey bestie 🫶 you found the <hotpink>tbl2asn</hotpink> page, and honestly? iconic. this is the tool that turns your sequence + feature table situation into a real GenBank submission, and she does not need you hand-feeding every record into Sequin like it's 2004. strap in. 💅

✨ NAME ✨

tbl2asn — prepare a GenBank submission using an ASCII feature table

no cap, that's the whole job description. 🎀

🌸 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]

look at all those little flags. she's giving alphabet soup 👑 every single one of them is real and every single one of them is below.

🦋 DESCRIPTION 🦋

okay so here's the tea, tbl2asn reads a template along with your sequence and table files, and outputs ASN.1 for submission to GenBank. that's it, that's the plot. ✨

and the reason this slaps? because you do not have to sit there and read each set of table and sequence files into Sequin one by one like some kind of Victorian orphan. 🙈

and it gets better — the template file can hold the organism and submitter information that's common to all your records, so you're not re-typing the same data for every single sequence/table pair. she said "DRY principle" and she meant it. 💅

🔥 OPTIONS 🔥

a summary of options is included below. (yes, all of them. we're doing this. hydrate first. 🍓)

• - — print usage message. that's it. a single lonely dash. she's mysterious, she's helpful.
• -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)
• -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
  • 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 — no description given. she's a mystery, she's an enigma, she's giving main character energy with zero backstory. 💀
• -z — Clean up log file Comment

heads up bestie: a couple of these are deprecated, and deprecated means "please use the new one instead" — -b wants you to use -V b, and -v wants you to use -V v. the old ones still show up to the party, but the cool kids moved on. 💅

👑 AUTHOR 👑

The National Center for Biotechnology Information.

(that's the whole author section. one line. she's concise, she's powerful, she ate. 🌈)

⭐ SEE ALSO ⭐

• Psequin(1)
• sbtedit(1)
• /usr/share/doc/ncbi-tools-bin/tbl2asn.txt.gz
• <http://www.ncbi.nlm.nih.gov/Sequin/table.html>

and that's the whole page, bestie 🎀 this one came to you straight from NCBI, dated 2016-09-01, and honestly she's still serving. now go submit something gorgeous. you've got this. 🦋✨