A summary of options is included below.
- Print usage message
-astr Accession
-Cstr Genome Center tag
-Dfilename
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-Gstr 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
-Hstr 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
-Mstr Master genome flags:
n Normal
b Big sequence
p Power option
t TSA
-Nn 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
-Vstr 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
-Xstr 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
-Yfilename
Read a comment string from filename-Zfilename
Write a discrepancy report to filename-astr 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 -Vb)
-cstr 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
-ffilename
Single table file
-g Input is a genomic product set
-h Convert general ID to note
-ifilename
Single input file
-jstr Source qualifiers
-kstr 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
-lstr 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
-mstr Lineage to use for discrepancy report tests
-nstr Organism name
-ofilename
Single output file
-pstr Path to files
-q Set sequence ID from input file name
-rstr Path for results
-s Read FASTAs as Set
-tfilename
Read template from filename-u Convert GenProdSet to NucProtSet
-v Validate (deprecated in favor of -Vv)
-wfilename
Single structured comment file (overrides the use of -XC)
-xstr Suffix (default = .fsa)
-ystr-z Clean up log file Comment
Install Now
PNG Icons
