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NCBI C Toolkit Cross Reference
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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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