NCBI C Toolkit Cross Reference

SEQUIN APPLICATION

Sequin 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.

Sequin 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.

Sequin 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.

Sequin 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.

Sequin runs on Macintosh, PC/Windows, UNIX and VMS computers and is available
by anonymous ftp from ftp.ncbi.nih.gov.


ADDING ANALYSIS PROGRAMS TO SEQUIN

The seqncfig file can be configured to add items to Sequin's Analysis menu.
Each section gives instructions on how to constuct a URL query to send to a
cgi program on the Internet. The cgi program is then responsible for running
the desired analysis program and for any necessary format conversions. A
sample cgi program written in C, testcgi.c, is in the demo directory of the
NCBI software toolkit. A perl version will be available soon. (Some analysis
programs could be modified to act as cgi programs directly, and for those
cases a separate cgi mediator program would not be necessary.)

A portion of a sample seqncfig file is shown below. Note that the section
names for the services are specified in the [ORDER] section, and items must
be of the form ORDER_1, ORDER_2,...ORDER_n.

    [ORDER]
    ORDER_1=tRNAscan
    ORDER_2=Seg
    ...

    [tRNAscan]
    HOST=www.myserver.myschool.edu
    PORT=80
    PATH=/MyServices/cgi-bin/testcgi.cgi
    QUERY=request=trnascan
    TITLE=tRNAscan-SE
    SUBMENU=Search
    FORMAT=FASTA
    FLAGS=SEQ,NUC,TRG,NET
    TIMEOUT=30

    [Seg]
    HOST=www.myserver.myschool.edu
    PORT=80
    PATH=/MyServices/cgi-bin/testcgi.cgi
    QUERY_1=request=seg
    TITLE_1=Seg default
    QUERY_2=request=seg&window=10&lowcut=1.0&hicut=1.5
    TITLE_2=Seg 10-1.0-1.5
    QUERY_3=request=seg&window=12&lowcut=2.3&hicut=2.6
    TITLE_3=Seg 12-2.3-2.6
    SUBMENU=Seg
    FORMAT=FASTA
    FLAGS=SEQ,DOC,PRT,TRG,NET
    TIMEOUT=30
    ...

    [ENZYMES]
    ENZ_1=BamHI
    ENZ_2=EcoRI
    ENZ_3=HindIII

The naming conventions for configuration files varies depending upon the
computer platform. For Mac it is seqncfig.cnf, for Windows seqncfig.ini, for
UNIX .seqncfigrc, and for VMS sequincfig.cfg. On the Mac, configuration files
go in the System Folder:Preferences folder, while for the PC they go in the
"windows" directory.

Individual configuration files may now be placed in a "services" directory
that is in the same directory as the Sequin program. They do not need to
conform to the naming convention described above.


SOLARIS EXECUTABLES

The Solaris executables distributed by NCBI no longer include a statically-
linked Motif library. This is due to the manner in which Sun distributes
Motif libraries. Users of Solaris version 2.4 and higher will find the
runtime shared Motif library on their system. Users of Solaris version 2.3
and earlier may need to either upgrade their systems or purchase the Motif
library separately.

It may be necessary to set your LD_LIBRARY_PATH environment variable to point
to the directory where this file, libXm.so.3 (the final digit may vary),
appears on your system. E.g.:

   setenv LD_LIBRARY_PATH /usr/dt/lib