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.TH PSEQUIN 1 2016-09-01 NCBI "NCBI Tools User's Manual"
.SH NAME
Psequin \- submit sequences to Genbank, EMBL, and DDBJ
.SH SYNOPSIS
.B Psequin
[\|\fB\-b\fP\|]
[\|\fB\-bse\fP\|]
[\|\fB\-e\fP\|]
[\|\fB\-f\fP\ \fIfilename\fP\|]
[\|\fB\-gc\fP\|]
[\|\fB\-h\fP\|]
[\|\fB\-oldaln\fP\|]
[\|\fB\-oldasn\fP\|]
[\|\fB\-oldgph\fP\|]
[\|\fB\-oldseq\fP\|]
[\|\fB\-oldsource\fP\|]
[\|\fB\-s\fP\|]
[\|\fB\-w\fP\|]
[\|\fB\-x\fP\|]
.SH DESCRIPTION
\fBPsequin\fP 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.
.PP
\fBPsequin\fP 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.
.PP
\fBPsequin\fP 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.
.PP
\fBPsequin\fP 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.
.SH OPTIONS
.TP
\fB\-b\fP
Bioseq-set mode
.TP
\fB\-bse\fP
binseqentry mode
.TP
\fB\-e\fP
Entrez mode
.TP
\fB\-f\fP\ \fIfilename\fP
read from \fIfilename\fP
.TP
\fB\-gc\fP
genome center mode
.TP
\fB\-h\fP
turn off automatic help
.TP
\fB\-oldaln\fP
use old alignment reader
.TP
\fB\-oldasn\fP
leave as old ASN.1
.TP
\fB\-oldgph\fP
use old graphic view
.TP
\fB\-oldseq\fP
use old sequence view
.TP
\fB\-oldsource\fP
use old flat-file source format
.TP
\fB\-s\fP
subtool mode
.TP
\fB\-w\fP
workbench mode
.TP
\fB\-x\fP
read from standard input
.SH AUTHOR
The National Center for Biotechnology Information.
.SH SEE ALSO
.ad l
.BR asnmacro (1),
.BR sbtedit (1),
.BR tbl2asn (1),
sequin.htm,
<http://www.ncbi.nlm.nih.gov/Sequin/>.
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