NCBI C Toolkit Cross Reference

C/sequin/


  Name Size Date (GMT) Description
Back   Parent directory   2017-09-23 03:33:12
File   README 4369  2001-12-12 20:53:02
File   macro.asn 35883  2016-01-05 22:19:17
C file   sbtedit.c 34378  2010-01-11 22:37:07
C file   sequin.h 76504  2014-12-23 14:45:05
C file   sequin1.c 1032330  2017-06-03 16:47:47
C file   sequin10.c 476232  2016-02-16 12:51:06
C file   sequin2.c 821403  2014-05-09 18:46:12
C file   sequin3.c 682414  2015-09-10 14:09:40
C file   sequin4.c 389051  2014-07-31 15:53:08
C file   sequin5.c 949993  2015-01-07 18:33:52
C file   sequin6.c 427784  2016-01-08 23:13:27
C file   sequin7.c 466832  2016-07-28 00:35:01
C file   sequin8.c 540163  2016-10-25 16:53:55
C file   sequin9.c 506045  2016-10-25 16:53:55
C file   sequinx.c 2371  1997-08-25 18:51:51
C file   sequiny.c 9534  2010-02-03 17:30:12
C file   sequiny.h 2936  1997-08-25 18:51:55
C file   streamer.c 46626  2010-09-02 16:58:51

  1 SEQUIN APPLICATION
  2 
  3 Sequin is a program designed to aid in the submission of sequences to the
  4 GenBank, EMBL, and DDBJ sequence databases. It was written at the National
  5 Center for Biotechnology Information, part of the National Library of
  6 Medicine at the National Institutes of Health.
  7 
  8 Sequin can assemble the essential elements of a GenBank record from simple
  9 FASTA-format text files. For example, the program obtains the proper genetic
 10 code from an organism name, and automatically determines coding region
 11 intervals by back-translation from the protein sequence. An on-line help
 12 window scrolls to the appropriate place as the user moves between and within
 13 data entry forms, giving relevant details on what information is expected.
 14 
 15 Sequin also contains a number of built-in validation functions for quality
 16 assurance. Features such as splice sites and coding region translations are
 17 checked for accuracy or internal consistency. Double-clicking on an error
 18 message launches an appropriate editor by which the user can correct any
 19 problems.
 20 
 21 Sequin provides live, clickable views of the data in a variety of formats,
 22 including a report form, GenBank flatfile, EMBL flatfile, and a graphical
 23 view. Double clicking on an item in any of these formats launches an editor
 24 for that item. The editor is capable of maintaining correct feature table
 25 positions as the underlying sequence is edited. It can display features on
 26 the sequence during editing, and allows feature intervals to be adjusted by
 27 direct manipulation.
 28 
 29 Sequin runs on Macintosh, PC/Windows, UNIX and VMS computers and is available
 30 by anonymous ftp from ftp.ncbi.nih.gov.
 31 
 32 
 33 ADDING ANALYSIS PROGRAMS TO SEQUIN
 34 
 35 The seqncfig file can be configured to add items to Sequin's Analysis menu.
 36 Each section gives instructions on how to constuct a URL query to send to a
 37 cgi program on the Internet. The cgi program is then responsible for running
 38 the desired analysis program and for any necessary format conversions. A
 39 sample cgi program written in C, testcgi.c, is in the demo directory of the
 40 NCBI software toolkit. A perl version will be available soon. (Some analysis
 41 programs could be modified to act as cgi programs directly, and for those
 42 cases a separate cgi mediator program would not be necessary.)
 43 
 44 A portion of a sample seqncfig file is shown below. Note that the section
 45 names for the services are specified in the [ORDER] section, and items must
 46 be of the form ORDER_1, ORDER_2,...ORDER_n.
 47 
 48     [ORDER]
 49     ORDER_1=tRNAscan
 50     ORDER_2=Seg
 51     ...
 52 
 53     [tRNAscan]
 54     HOST=www.myserver.myschool.edu
 55     PORT=80
 56     PATH=/MyServices/cgi-bin/testcgi.cgi
 57     QUERY=request=trnascan
 58     TITLE=tRNAscan-SE
 59     SUBMENU=Search
 60     FORMAT=FASTA
 61     FLAGS=SEQ,NUC,TRG,NET
 62     TIMEOUT=30
 63 
 64     [Seg]
 65     HOST=www.myserver.myschool.edu
 66     PORT=80
 67     PATH=/MyServices/cgi-bin/testcgi.cgi
 68     QUERY_1=request=seg
 69     TITLE_1=Seg default
 70     QUERY_2=request=seg&window=10&lowcut=1.0&hicut=1.5
 71     TITLE_2=Seg 10-1.0-1.5
 72     QUERY_3=request=seg&window=12&lowcut=2.3&hicut=2.6
 73     TITLE_3=Seg 12-2.3-2.6
 74     SUBMENU=Seg
 75     FORMAT=FASTA
 76     FLAGS=SEQ,DOC,PRT,TRG,NET
 77     TIMEOUT=30
 78     ...
 79 
 80     [ENZYMES]
 81     ENZ_1=BamHI
 82     ENZ_2=EcoRI
 83     ENZ_3=HindIII
 84 
 85 The naming conventions for configuration files varies depending upon the
 86 computer platform. For Mac it is seqncfig.cnf, for Windows seqncfig.ini, for
 87 UNIX .seqncfigrc, and for VMS sequincfig.cfg. On the Mac, configuration files
 88 go in the System Folder:Preferences folder, while for the PC they go in the
 89 "windows" directory.
 90 
 91 Individual configuration files may now be placed in a "services" directory
 92 that is in the same directory as the Sequin program. They do not need to
 93 conform to the naming convention described above.
 94 
 95 
 96 SOLARIS EXECUTABLES
 97 
 98 The Solaris executables distributed by NCBI no longer include a statically-
 99 linked Motif library. This is due to the manner in which Sun distributes
100 Motif libraries. Users of Solaris version 2.4 and higher will find the
101 runtime shared Motif library on their system. Users of Solaris version 2.3
102 and earlier may need to either upgrade their systems or purchase the Motif
103 library separately.
104 
105 It may be necessary to set your LD_LIBRARY_PATH environment variable to point
106 to the directory where this file, libXm.so.3 (the final digit may vary),
107 appears on your system. E.g.:
108 
109    setenv LD_LIBRARY_PATH /usr/dt/lib

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