OnWorks favicon

asn2gb - Online in the Cloud

Run asn2gb in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command asn2gb that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



asn2gb - convert ASN.1 biological data to a GenBank-style flat format


asn2gb [-] [-A accession] [-F] [-a asn-type] [-b] [-c] [-d] [-f format] [-g N] [-h N]
[-i filename] [-j N] [-k N] [-l filename] [-m mode] [-n filename] [-o filename] [-p]
[-q filename] [-r] [-s style] [-t N] [-u N] [-y N]


asn2gb converts descriptions of biological sequences from NCBI's ASN.1 format to one of
several flat-file formats, and is the successor to asn2ff(1).


A summary of options is included below.

- Print usage message

-A accession
Accession to fetch; may take the form accession,complexity,flags where complexity
should normally be 0 and a flags value of -1 enables fetching of external features
(as with the legacy -F option)

-F Fetch remote annotations (equivalent to specifying -A accession,0,-1)

-a asn-type
ASN.1 Type:
[Single record]
a Any (autodetected; default)
e seq-Entry
b Bioseq
s bioseq-Set
m seq-subMit
q Catenated
[Release file; components individually processed and freed]
t baTch bioseq-set
u batch seq-sUbmit

-b Input file is binary

-c Batch file is compressed

-d Seq-loc minus strand

-f format
b GenBank (default)
bp or pb
GenBank and GenPept
p GenPept
q nucleotide GBSet (XML)
r protein GBSet (XML)
t Feature table only
x nucleotide INSDSet (XML)
y tiny seq (XML)
z protein INSDSet (XML)

-g N Bit flags (all default to off):
4 ContigFeats
8 ContigSrcs
16 FarTransl

-h N Lock/Lookup Flags (all default to off):
8 LockProd
16 LookupComp
64 LookupProd

-i filename
Input file name (default = stdin)

-j N Start location (default is 0, beginning of sequence)

-k N End location (default is 0, end of sequence)

-l filename
Log file

-m mode
r Release
e Entrez
s Sequin (default)
d Dump

-n filename
Asn2Flat Executable (default = asn2flat)

-o filename
Output file name (default = stdout)

-p Propagate top descriptors

-q filename
Ffdiff Executable (default = /netopt/genbank/subtool/bin/ffdiff)

-r Enable remote fetching

-s style
n Normal (default)
s Segment
m Master
c Contig

-t N Batch:
1 Report
2 Sequin/Release
3 asn2gb SSEC/nocleanup
4 asn2flat BSEC/nocleanup
5 asn2gb/asn2flat
6 asn2gb NEW dbxref/OLD dbxref
7 oldasn2gb/newasn2gb
-u N Custom flags (all default to off):
4 Hide features
1792 Hide references
8192 Hide sources
262144 Hide translations

-y N Feature itemID

Use asn2gb online using onworks.net services