407 lines
18 KiB
Text
407 lines
18 KiB
Text
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FEATURES.DOC update 7 Feb 94
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NAME
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FEATURES - extracts features from GenBank entries
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SYNOPSIS
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features
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features expression
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features [-f featurekey | -F keyfile]
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[-n name |-a accession | -e expression |
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-N namefile |-A accfile | -E expfile]
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[-u dbfile | -U dbfile | -g ]
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features -h
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DESCRIPTION
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FEATURES extracts sequence objects from GenBank entries, using
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the Features Table language. Features can be retrieved either by
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specifying keywords (eg. CDS, mRNA, exon, intron etc.) or by
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evaluating expressions. In practical terms, FEATURES is actually
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a user interface for GETOB, which actually performs the parsing
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and extraction of sequence objects. FEATURES can be run either as
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an interactive program or with command line arguments.
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'features' with no arguments runs the program interactively.
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'features' followed by an expression retrieves the data directly
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from GenBank and evaluates the expression. The third form of
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features requires all arguments to be accompanied by their
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respective option flags. Finally, 'features -h' prints the
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SYNOPSIS.
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INTERACTIVE EXECUTION
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FEATURES executed with no arguments runs interactively. An example of the
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FEATURES menu is shown below:
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___________________________________________________________________
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FEATURES - Version 7 FEB 94
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Please cite: Fristensky (1993) Nucl. Acids Res. 21:5997-6003
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___________________________________________________________________
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Features: tRNA
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Entries: EPFCPCG
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Dataset:
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___________________________________________________________________
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Parameter Description Value
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-------------------------------------------------------------------
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1).................... FEATURES TO EXTRACT ....................> f
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f:Type a feature at the keyboard
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F:Read a list of features from a file
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2)....................ENTRIES TO BE PROCESSED (choose one).....> n
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Keyboard input - n:name a:accession # e:expression
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File input - N:name(s) A:accession #(s) E:expression(s)
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3)....................WHERE TO GET IT .........................> g
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u:Genbank dataset g:complete GenBank database
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U: same as u, but all entries
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4)....................WHERE TO SEND IT ........................> a
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s:Each feature to a separate file a:All output to same file
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---------------------------------------------------------------
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Type number of your choice or 0 to continue:
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0
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Messages will be written to EPFCPCG.msg
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Final sequence output will be written to EPFCPCG.out
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Expressions will be written to EPFCPCG.exp
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Extracting features...
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In the example, FEATURES was instructed to retrieve all tRNAs from
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the GenBank entry EPFCPCG, which contains the Epifagus plastid
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genome. By default, the GenBank database was the source of the
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sequence. Messages indicate the progress of the job. A log describing
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the extraction of each feature is written to EPFCPCG.msg, while the
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extracted features themselves are written to EPFCPCG.out. Feature
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expressions which could be used by FEATURES to reconstruct the .out
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file, are written to EPFCPCG.exp.
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The first step is to retrieve the EPFCPCG entry from GenBank, which is
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accomplished by calling FETCH. Next, FEATURES extracts the specified
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features from the entry.
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An excerpt from EPFCPCG.msg is shown below, describing the extraction
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of the fifth tRNA found in this entry. To create this tRNA, two exons
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had to be joined. The qualifier line associated with this feature
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indicates that it is an Isoleucine tRNA with a gat anticodon.
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EPFCPCG:anticodon gtg
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complement
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(
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join
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(
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70023 70028
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1 69
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)
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)
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/product="transfer RNA-His"
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/gene="His-tRNA"
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/label=anticodon gtg
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/note="anticodon gtg"
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//----------------------------------------------
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The actual sequence for this feature, as written to EPFCPCG.out, is
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written with each exon beginning a new line:
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>EPFCPCG:anticodon gtg
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ggcggatgtagccaaatggatcaaggtagtggattgtgaatccaacatat
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gcgggttcaattcccgtcg
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ttcgcc
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Finally, the expression that was evaluated to create this feature is
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written to EPFCPCG.exp:
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>EPFCPCG:anticodon gtg
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@M81884:anticodon gtg
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If EPFCPCG.exp was used as an expression file in option 2 (E) of FEATURES,
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EPFCPCG.out would be recreated.
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OPTIONS
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1) FEATURES - choosing f will cause FEATURES to prompt for
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a feature to extract. If you wish to extract several types of
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features simultaneously (ie. F), you must construct a file listing the
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feature keywords. The following example would retrieve both tRNA and
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rRNA sequences:
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OBJECTS
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tRNA
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rRNA
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SITES
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The words 'OBJECTS' and 'SITES' must enclose the feature keywords,
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and each keyword must be on a separate line. For a rigorous
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definition of the input file format, see the GETOB manual pages
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(getob.doc).
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In the menu shown above, f was chosen, and the user entered tRNA at
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the prompt. Thus tRNA is now displayed on the Features: line. If
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features had been specified from a file (suboption F) then the
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filename containing the feature keywords would be displayed instead.
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A complete list of legal feature keywords can be found in the GenBank
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Release notes (gbrel.txt) under the subheading 'Feature Key Names'.
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2) ENTRIES
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n User is prompted for the name of an entry from which the
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feature is to be extracted. The name of the entry will appear
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on the 'Entries' line of the menu.
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N User is prompted for a filename containing one or more
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entry names. Each name must be on a separate line. The filename
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will be displayed on the 'Entries' menu line.
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a User is prompted for an accession number, which will appear
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on the 'Entries' line of the menu.
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A User is prompted for a filename for accession numbers. The filename
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will appear on the 'Entries:' line.
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e User is prompted for a GenBank Features expression of the
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form accession:location.'accession' refers to a GenBank
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accession number, while 'location' is any legal feature location.
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A brief description of location syntax can be found under the
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subheading "Feature Location" in the GenBank release notes
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(gbrel.txt). See "The DDBJ/EMBL/GenBank Feature Table:
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Definition" Version 1.04 for a complete definition.
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E User is prompted for a filename containing one or more Feature
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expressions. EACH EXPRESSION MUST BEGIN A '@'. All lines beginning
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with '@' are processed as expressions, and all other lines are
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copied to the output file unchanged.
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Examples:
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The tRNA shown above could have been extracted by choosing
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suboption e and entering either of the following expressions:
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M81884:complement(join(70023..70028,1..69))
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M81884:anticodon gtg
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In the first example, the feature line from the original entry
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is used as the location. In the second example, the feature is
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found by its qualifier line, which also appeared in the
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original entry. It must be noted that the qualifier line must
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be unique from others in the same entry in its first 15
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characters after the = .
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The flaL protein coding region of B. licheniformis is described
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in GenBank entry BLIFALA, accession number M60287 in the
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following feature:
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CDS 305..640
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/note="flaD (sin) homologue"
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/gene="flaL"
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/label=ORF2
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/codon_start=1
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This feature could be retrieved using any of the following
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expressions:
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M60287:305..640
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M60287:ORF2
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M60287:/label=ORF2
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M60287:/gene="flaL"
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M60287:/note="flaD (sin) homologue"
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Note that the /label= qualifier is special, in that labels are
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specifically intented as unique tags on an feature. For labels,
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only the label itself is need be specified. Thus, /label=ORF2 is
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equivalent to ORF2. For other qualifiers, the qualifier keyword
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(eg. /note=) must be included.
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3) DATABASE (WHERE TO GET IT) - By default, all entries processed will
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be automatically retrieved from GenBank using FETCH. Specifying 'u'
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(User-defined database subset) makes it possible to extract features
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from GenBank subsets created by the user. Usually, retrieval of
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features is much faster with a User-defined subset, so if you
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frequently work with sets of genes, it is best to retrieve them
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en-masse using FETCH, and work with them directly. For example, if
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you had retrieved a set of Beta-globin sequences into a file called
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'globin.gen', you could directly extract features from these entries
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by specifying 'globin' or 'globin.gen' as your User-defined database.
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If the file extension is '.gen', FEATURES will automatically create
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temporary files called globin.ano, globin.wrp and globin.ind,
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containing annotation, sequence, and an index, respectively. These
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files will be read during feature extraction, and then discarded. If
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you have already created such files using SPLITDB, simply specify
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any of 'globin', 'globin.ano', etc. ie. anything, as long as it does
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not have the .gen file extension.
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'U' rather than 'u' causes ALL entries in the user-defined
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database to be subset. This means that it is unnecessary to
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specify entry options (eg -n, -N etc.), as these will be
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ignored, if given.
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One consequence of these conventions is that the individual GenBank
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divisions can be processed directly. For example, suppose you were only
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interested in rodent globins. You could directly access the rodent
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division of GenBank by specifying the base name of that file division
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(eg. /home/psgendb/GenBank/gbrod) as your user-defined database. In
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this case, the files gbrod.ano, gbrod.wrp and gbrod.ind already
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exist. Again, this approach is faster, since FEATURES would not have
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to find and retrieve the sequences, but can read directly from the
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database files. Finally, if you wanted to process all of the entries
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in the database division, simply use -U. The user is warned that a
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GenBank division is a huge amount of data, and processing every entry
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could take a long time.
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4) WHERE TO SEND IT - By default (a), the output for all entries goes
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to a single set of files, whose names are chosen by FEATURES,
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depending on the setting of option 2, Entries. If a single name (n) or
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accession number (a) has been chosen, that will be used as
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the raw filename. For example, if you were processing the entry
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WHTCAB, the output files would be WHTCAB.msg and WHTCAB.out. If names
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(N), accession numbers (A) or expressions (E) were read from a file,
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the raw name of that file would be used eg. cellulase.nam would result
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in cellulase.msg and cellulase.out. Finally, if a single expression
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is processed (e), then the primary accession number in that
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expression will be used for the filenames. In all cases, FEATURES
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will tell you the names of the files being written.
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Choosing suboption s, you can specify that the features created for
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each entry be sent to separate files. In this case, each file will
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have the name of that entry, with the extension .obj. However, all
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messages and expressions will still go to a single files. While this
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can be a convenient way of creating separate files when you need them,
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this option still has the limitation of writing all features for a
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given entry (if there are more than one) to the same file. Also,
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successive resolution of features (anything requiring 'getob -r')
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will not work with this option. This may be corrected in future
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versions.
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COMMAND LINE EXECUTION
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There are two ways of running FEATURES from the command line. If only one
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argument is supplied, that argument is interpreted as an expression, and
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the result of that expression (ie. a sequence ) is written to the
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standard output. .msg, .out and .exp files are NOT created. For example,
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GenBank entry BACFLALA (M60287) contains the following feature:
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CDS 95..271
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/label=LORF-
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/codon_start=1
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/translation="MNKDKNEKEELDEEWTELIKHALEQGISPDDIRIFLNLGKKSSK
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PSASIERSHSINPF"
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Any of
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features M60287:LORF-
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features M60287:95..271
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features M60287:/label=LORF-
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would write the open reading frame to the standard output:
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atgaataaagataaaaatgagaaagaagaattggatgaggagtggacaga
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actgattaaacacgctcttgaacaaggcattagtccagacgatatacgta
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tttttctcaatttgggtaagaagtcttcaaaaccttccgcatcaattgaa
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agaagtcattcaataaatcctttctga
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This form of FEATURES is provided to make it easy to pipe output to
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other programs for further processing. For example
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features M60287:LORF- |ribosome >LORF.protein
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would write the translation of the open reading frame to a file called
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LORF.protein.
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The full functionality of the FEATURES can be accessed using arguments on
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the command line. In particular, when there are multiple entries to be
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processed, or multiple features within entries, it is much faster to
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supply FEATURES with lists of entries, feature keys or expressions.
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Command line options are similar to suboptions in menu items 1-3 above:
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Feature keys:
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-f key {feature key}
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-F filename {file of feature keys}
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Entries:
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-n name {GenBank LOCUS name}
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-N filename {file of GenBank LOCUS names}
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-a accession {GenBank ACCESSION number}
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-A filename {file of GenBank ACCESSION numbers}
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-e expression {Feature Table expression}
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-E filename {file of Feature Table expressions, each begin-
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ning with '@'}
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Databases:
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-u filename {GenBank dataset}
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-U filename { " " " " " " ,
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process all entries ie. -nNaAeE options
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will be ignored}
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-g {GenBank}
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Examples:
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features -f tRNA -n EPFCPCG
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retrieves all tRNAs from GenBank entry EPFCPCG and writes .msg, .out,
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and .exp files.
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features -e M60287:LORF-
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would retrieve the same open reading frame as in the earlier example.
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Since most time-consuming operation in FEATURES is sequence retrieval,
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it is often best to retrieve frequently-used sequences as database
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subsets. For example, a set GenBank entries for chlorophyl a/b binding
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protein genes might be stored in a file called CAB.gen.
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features -f CDS -N CAB.nam -u CAB.gen
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would generate the files CAB.msg, CAB.out and CAB.exp containing output
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for all CDS features in the entries listed in the file CAB.nam.
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features -E CAB.exp -u CAB.gen
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would re-create the output file CAB.out.
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BUGS
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FEATURES does no preliminary error checking for syntax of
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GenBank expressions prior to their evaluation. Expressions that can
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not be evaluated will be flagged by GETOB in the .msg file.
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At present, little checking is done to test for the presence or
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correctness of input files. Some errors may cause the program to
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crash.
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For User-defined datasets, filename expansion is not performed.
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FILES
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Temporary files:
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X.term X.ano X.wrp X.ind X.gen {X is raw filename, see 4) }
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UNRESOLVED.fea UNRESOLVED.out
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FEA.inf FEA.nam FEA.gen FEA.ano FEA.wrp FEA.ind FEA.msg FEA.out
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SEE ALSO
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grep(1V) fetch getob splitdb
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TRANSPORTATION NOTES
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It should be fairly easy to get FEATURES to work even on systems
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in which GenBank has not been formatted for the XYLEM package.
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This is because FEATURES does not work directly on the database, but
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rather retrieves all necessary sequences by calling FETCH. Thus,
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statements like 'fetch FEA.nam FEA.gen' could be replaced with any
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command that, given a file containing names or accession numbers,
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returns a file containing GenBank entries. In principle, you
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could even implement this sort of command to retrieve entries from
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the email server (retrieve@ncbi.nlm.nih.gov) at NCBI, although
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such a setup would undoubtedly be quite slow.
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AUTHOR
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Dr. Brian Fristensky
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Dept. of Plant Science
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University of Manitoba
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Winnipeg, MB Canada R3T 2N2
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Phone: 204-474-6085
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FAX: 204-261-5732
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frist@cc.umanitoba.ca
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REFERENCE
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Fristensky, B. (1993) Feature expressions: creating and manipulating
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sequence datasets. Nucleic Acids Research 21:5997-6003.
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