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showfeat |
% 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 then 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 wish to show. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from. The source may be wildcarded by using '*'. If you wish to show more than one source, separate their names with the character '|', eg: 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 wish to show. See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot feature types. The type may be wildcarded by using '*'. If you wish to show more than one type, separate their names with the character '|', eg: *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, for example '/gene' can have the value of the gene name. By default any feature tag in the feature table is shown. You can set this to match any feature tag you wish to show. The tag may be wildcarded by using '*'. If you wish to show more than one tag, separate their names with the character '|', eg: 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'. Only some of these tags can have values, for example '/gene' can have the value of the gene name. By default any feature tag value in the feature table is shown. You can set this to match any feature tag valueyou wish to show. The tag value may be wildcarded by using '*'. If you wish to show more than one tag value, separate their names with the character '|', eg: pax* | 10 -sort menu Sort features by Type, Start or Source, Nosort (don't sort - use input order) or 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 be false if you do not wish to display the ID name of the sequence. -[no]description boolean Set this to be false if you do not wish to display the description of the sequence. -[no]scale boolean Set this to be false if you do not wish 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 would cover a standard page width and a width a 10 characters would be 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 this is set, then 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 type 'exon' in the same sense, then they will all be displayed on the same line. This makes it hard to distinguish overlapping features. If this is set to false then each feature is displayed on a separate line making it easier to distinguish where features start and end. -[no]forward boolean Set this to be false if you do not wish to display forward sense features. -[no]reverse boolean Set this to be false if you do not wish to display reverse sense features. -[no]unknown boolean Set this to be false if you do not wish to display unknown sense features. (ie. features with no directionality - all protein features are of this type and some nucleic features (for example, CG-rich regions)). -strand boolean Set this if you wish 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 wish 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 (eg: EMBL) that the feature came from. -position boolean Set this if you wish to display the start and end position of the features. If several features are being displayed on the same line, then the start and end positions will be joined by a comma, for example: '189-189,225-225'. -[no]type boolean Set this to be false if you do not wish to display the type of the features. -tags boolean Set this to be false if you do not wish to display the tags and values of the features. -[no]values boolean Set this to be false if you do not wish to display the tag values of the features. If this is set to be false, only the tag names will be displayed. If the tags are not displayed, then the values will not be displayed. The value of the 'translation' tag is never displayed as it is often extremely long. General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required | ||||||||||
[-outfile] (Parameter 2) |
If you enter the name of a file here then this program will write the feature details into that file. | Output file | <sequence>.showfeat | ||||||||||
Optional qualifiers | Allowed values | Default | |||||||||||
-matchsource | By default any feature source in the feature table is shown. You can set this to match any feature source you wish to show. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from. The source may be wildcarded by using '*'. If you wish to show more than one source, separate their names with the character '|', eg: gene* | embl | Any string is accepted | * | ||||||||||
-matchtype | By default any feature type in the feature table is shown. You can set this to match any feature type you wish to show. See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot feature types. The type may be wildcarded by using '*'. If you wish to show more than one type, separate their names with the character '|', eg: *UTR | intron | Any string is accepted | * | ||||||||||
-matchtag | 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, for example '/gene' can have the value of the gene name. By default any feature tag in the feature table is shown. You can set this to match any feature tag you wish to show. The tag may be wildcarded by using '*'. If you wish to show more than one tag, separate their names with the character '|', eg: gene | label | Any string is accepted | * | ||||||||||
-matchvalue | 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'. Only some of these tags can have values, for example '/gene' can have the value of the gene name. By default any feature tag value in the feature table is shown. You can set this to match any feature tag valueyou wish to show. The tag value may be wildcarded by using '*'. If you wish to show more than one tag value, separate their names with the character '|', eg: pax* | 10 | Any string is accepted | * | ||||||||||
-sort | Sort features by Type, Start or Source, Nosort (don't sort - use input order) or join coding regions together and leave other features in the input order |
|
start | ||||||||||
Advanced qualifiers | Allowed values | Default | |||||||||||
-html | Use HTML formatting | Yes/No | No | ||||||||||
-[no]id | Set this to be false if you do not wish to display the ID name of the sequence. | Yes/No | Yes | ||||||||||
-[no]description | Set this to be false if you do not wish to display the description of the sequence. | Yes/No | Yes | ||||||||||
-[no]scale | Set this to be false if you do not wish to display the scale line. | Yes/No | Yes | ||||||||||
-width | 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 would cover a standard page width and a width a 10 characters would be nearly unreadable. If the width is set to less than 4, the graphics lines and the scale line will not be displayed. | Integer 0 or more | 60 | ||||||||||
-collapse | If this is set, then 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 type 'exon' in the same sense, then they will all be displayed on the same line. This makes it hard to distinguish overlapping features. If this is set to false then each feature is displayed on a separate line making it easier to distinguish where features start and end. | Yes/No | No | ||||||||||
-[no]forward | Set this to be false if you do not wish to display forward sense features. | Yes/No | Yes | ||||||||||
-[no]reverse | Set this to be false if you do not wish to display reverse sense features. | Yes/No | Yes | ||||||||||
-[no]unknown | Set this to be false if you do not wish to display unknown sense features. (ie. features with no directionality - all protein features are of this type and some nucleic features (for example, CG-rich regions)). | Yes/No | Yes | ||||||||||
-strand | Set this if you wish to display the strand of the features. Protein features are always directionless (indicated by '0'), forward is indicated by '+' and reverse is '-'. | Yes/No | No | ||||||||||
-source | Set this if you wish 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 (eg: EMBL) that the feature came from. | Yes/No | No | ||||||||||
-position | Set this if you wish to display the start and end position of the features. If several features are being displayed on the same line, then the start and end positions will be joined by a comma, for example: '189-189,225-225'. | Yes/No | No | ||||||||||
-[no]type | Set this to be false if you do not wish to display the type of the features. | Yes/No | Yes | ||||||||||
-tags | Set this to be false if you do not wish to display the tags and values of the features. | Yes/No | No | ||||||||||
-[no]values | Set this to be false if you do not wish to display the tag values of the features. If this is set to be false, only the tag names will be displayed. If the tags are not displayed, then the values will not be displayed. The value of the 'translation' tag is never displayed as it is often extremely long. | Yes/No | Yes |
Here is the file:
FH Key Location/Qualifiers FH FT source 1..2167 FT /db_xref="taxon:287" FT /organism="Pseudomonas aeruginosa" FT /strain="PAC" FT /isolate="PAC 1" FT /map="38 min" FT CDS 1289..1879 FT /db_xref="SWISS-PROT:P10932" FT /note="aliphatic amidase regulator, positive regulator of FT amiE" FT /transl_table=11 FT /gene="amiR" FT /protein_id="CAA32023.1" FT /translation="MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPP FT PEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHG FT VITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWD FT EREAHQHLSREAMKRREPILKIAQELLGNEPSA" FT CDS 135..1292 FT /db_xref="SWISS-PROT:P27017" FT /note="negative regulator of amiR" FT /transl_table=11 FT /gene="amiC" FT /protein_id="CAA32024.1" FT /translation="MGSHQERPLIGLLFSETGVTADIERSHAYGALLAVEQLNREGGVG FT GRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCY FT PTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHL FT YRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYG FT DGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFVQACHGFFPENAT FT ITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSS FT RIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP" FT promoter 8..24 FT /note="proposed rpoN-dependent promoter" FT promoter 65..81 FT /note="proposed rpoN-dependent promoter" FT RBS 121..126 FT /note="proposed Shine-Dalgarno sequence" FT mutation 912..1167 FT /note="ClaI fragment deleted in pSW36, constitutive FT phenotype" FT /replace="" FT /gene="amiC" FT misc_feature 1 FT /note="last base of an XhoI site" FT misc_feature 648..653 FT /note="end of 658bp XhoI fragment, deletion in pSW3 causes FT constitutive expression of amiE" FT conflict 1281 FT /replace="g" FT /citation=[3]
Here is the output from the example run:
|==========================================================| 2167 > misc_feature |----------------------------------------------------------> source > promoter |> promoter > RBS |-------------------------------> CDS |> misc_feature |------> variation > conflict |----------------> CDS
Program name | Description |
---|---|
abiview | Reads ABI file and display the trace |
cirdna | Draws circular maps of DNA constructs |
coderet | Extract CDS, mRNA and translations from feature tables |
extractfeat | Extract features from a sequence |
lindna | Draws linear maps of DNA constructs |
maskfeat | Mask off features of a sequence |
pepnet | Displays proteins as a helical net |
pepwheel | Shows protein sequences as helices |
prettyplot | Displays aligned sequences, with colouring and boxing |
prettyseq | Output sequence with translated ranges |
remap | Display a sequence with restriction cut sites, translation etc |
seealso | Finds programs sharing group names |
showalign | Displays a multiple sequence alignment |
showdb | Displays information on the currently available databases |
showseq | Display a sequence with features, translation etc |
swissparse | Retrieves sequences from swissprot using keyword search |
textsearch | Search sequence documentation text. SRS and Entrez are faster! |
Dec 2001 - added -sort nosort option to get the features in the input order