showfeat

showfeat

showfeat reads a protein or nucleic sequence and its feature table and writes a text representation of the features to standard output.

Here is a sample session with showfeat. The feature table is specified as a -ufo qualifier (uniform feature object) in this case, a file containing an EMBL feature table:

% showfeat em:paamir Show features of a sequence. Output file [paamir.showfeat]: stdout PAAMIR Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation |=   =  =    =  =  =  =  =  =  =  =   =  =  =  =  =  =  =  =  | 2167 >                                                           misc_feature |---------------------------------------------------------> source >                                                           promoter |>                                                          promoter   >                                                         RBS   |------------------------------->                         CDS                 |>                                          misc_feature                         |------>                            variation                                   >                         conflict                                   |---------------->        CDS

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

[-outfile] (outfile)

If you enter the name of a file here, this program will write the feature details into that file.

Optional qualifiers:

-matchsource (string)

By default, any feature source in the feature table is shown. You can set this to match any feature source you want to show. The source name is usually the name of the program that detected the feature, or the feature table (e.g., EMBL) that the feature came from. The source may be wildcarded by using *. If you want to show more than one source, separate their names with the | character. For example:

gene* | embl
-matchtype (string)

By default, any feature type in the feature table is shown. You can set this to match any feature type you want to show. See Chapter 2 for a list of the EMBL feature types, and Chapter 3 for a list of the SWISS-PROT feature types. The type may be wildcarded using *. If you want to show more than one type, separate their names with the | character. For example:

*UTR | intron
-matchtag (string)

Tags are the types of extra values that a feature may have. For example, in the EMBL feature table, a CDS type of feature may have the tags /codon, /codon_start, /db_xref, /EC_number, /evidence, /exception, /function, /gene, /label, /map, /note, /number, /partial, /product, /protein_id, /pseudo, /standard_name, /translation, /transl_except, /transl_table, or /usedin. Some of these tags also have values (e.g., /gene can have the value of the gene name). By default, any feature tag in the feature table is extracted. You can set this to match any feature tag you want to show. The tag may be wildcarded by using *. If you want to extract more than one tag, separate their names with the | character. For example:

gene | label
-matchvalue (string)

Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. For example, in the EMBL feature table, a CDS type of feature may have the tags /codon, /codon_start, /db_xref, /EC_number, /evidence, /exception, /function, /gene, /label, /map, /note, /number, /partial, /product, /protein_id, /pseudo, /standard_name, /translation, /transl_except, /transl_table, or /usedin. Some of these tags also have values (e.g., /gene can have the value of the gene name). By default, any feature tag in the feature table is extracted. You can set this to match any feature tag value you want to show. The tag may be wildcarded by using *. If you want to extract more than one tag, separate their names with the | character. For example:

pax* | 10
-sort (menu)

Sort features by Type, Start, or Source. Nosort uses the input order and does not sort. This qualifier can also be used to join coding regions together and leave other features in the input order.

Advanced qualifiers:

-html (boolean)

Use HTML formatting.

-[no]id (boolean)

Set this to false if you do not want to display the ID name of the sequence.

-[no]description (boolean)

Set this to false if you do not want to display the description of the sequence.

-[no]scale (boolean)

Set this to false if you do not want to display the scale line.

-width (integer)

You can expand (or contract) the width of the ASCII-character graphics display of the positions of the features using this value. For example, a width of 80 characters covers a standard page width, while a width a 10 characters is nearly unreadable. If the width is set to less than 4, the graphics lines and the scale line will not be displayed.

-collapse (boolean)

If set, features from the same source and of the same type and sense are all printed on the same line. For instance, if there are several features from the EMBL feature table (ie. the same source) which are all of the type "exon" in the same sense, they will all be displayed on the same line. This makes it hard to distinguish overlapping features. If this is set to false, each feature is displayed on a separate line. This makes it easier to distinguish where features start and end.

-[no]forward (boolean)

Set this to false if you do not want to display forward sense features.

-[no]reverse (boolean)

Set this to false if you do not want to display reverse sense features.

-[no]unknown (boolean)

Set this to false if you do not want to display unknown sense features. For example, features with no directionality (all protein features are of this type) and some nucleic features (such as CG-rich regions).

-strand (boolean)

Set this if you want to display the strand of the features. Protein features are always directionless (indicated by 0), forward is indicated by +, and reverse is -.

-source (boolean)

Set this if you want to display the source of the features. The source name is usually either the name of the program that detected the feature or it is the name of the feature table (e.g., EMBL) that the feature came from.

-position (boolean)

Set this if you want to display the start and end position of the features. If several features are being displayed on the same line, the start and end positions will be joined by a comma. For example: 189-189,225-225.

-[no]type (boolean)

Set this to false if you do not want to display the type of the features.

-tags (boolean)

Set this to false if you do not want to display the tags and values of the features.

-[no]values (boolean)

Set this to false if you do not want to display the tag values of the features. If this is set to false, only the tag names are displayed. If the tags are not displayed, the values will not be displayed. Because the value of the translation tag is often very long, it is never displayed.



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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