Psequin - submit sequences to Genbank, EMBL, and DDBJ
Psequin [
-b] [
-bse] [
-e] [
-f filename] [
-gc] [
-h] [
-oldaln]
[
-oldasn] [
-oldgph] [
-oldseq] [
-oldsource] [
-s] [
-w] [
-x]
Psequin is a program designed to aid in the submission of sequences to
the GenBank, EMBL, and DDBJ sequence databases. It was written at the National
Center for Biotechnology Information, part of the National Library of Medicine
at the National Institutes of Health.
Psequin can assemble the essential elements of a GenBank record from
simple FASTA-format text files. For example, the program obtains the proper
genetic code from an organism name, and automatically determines coding region
intervals by back-translation from the protein sequence. An on-line help
window scrolls to the appropriate place as the user moves between and within
data entry forms, giving relevant details on what information is expected.
Psequin also contains a number of built-in validation functions for
quality assurance. Features such as splice sites and coding region
translations are checked for accuracy or internal consistency. Double-clicking
on an error message launches an appropriate editor by which the user can
correct any problems.
Psequin provides live, clickable views of the data in a variety of
formats, including a report form, GenBank flatfile, EMBL flatfile, and a
graphical view. Double clicking on an item in any of these formats launches an
editor for that item. The editor is capable of maintaining correct feature
table positions as the underlying sequence is edited. It can display features
on the sequence during editing, and allows feature intervals to be adjusted by
direct manipulation.
- -b
- Bioseq-set mode
- -bse
- binseqentry mode
- -e
- Entrez mode
-
-f filename
- read from filename
- -gc
- genome center mode
- -h
- turn off automatic help
- -oldaln
- use old alignment reader
- -oldasn
- leave as old ASN.1
- -oldgph
- use old graphic view
- -oldseq
- use old sequence view
- -oldsource
- use old flat-file source format
- -s
- subtool mode
- -w
- workbench mode
- -x
- read from standard input
The National Center for Biotechnology Information.
asnmacro(1),
sbtedit(1),
tbl2asn(1),
/usr/share/doc/ncbi-tools-x11/sequin.htm,
<
http://www.ncbi.nlm.nih.gov/Sequin/>.