|
twofeat |
Function
Finds neighbouring pairs of features in sequencesDescription
twofeat reads in the feature tables of sequences and reports occurances of pairs of specified features.This is intended for use as a simple data-mining tool to enable you to look for instances of pairs of features that occur near to each other in the same sequence entry.
For each of the pair of features, you can specify its type name, its sense, its score and any tag/value pairs, amongst other things.
You can then specify the type of relationship that the two features should have. You can specify the minimum and maximum distance between them. You can specify the type of overlap allowed: Any type of overlap or no overlap is allowed, Overlap required, No overlaps are allowed, Overlap required but one feature must not be completely within the other, Feature A must be completely enclosed within feature B, Feature B must be completely enclosed within feature A. You can specify that the distance should be measured from the nearest ends of the two features, From the left ends, From right ends, From the furthest ends. You can specify that the features should be in any sense, in the same sense or in opposite senses. You can specify that the features should be in any order, Feature A then feature B, Feature B then feature A.
By default the resulting pairs of features found are then written to a report file as a single feature from the first postion of the left-most feature to the last position of the right-most feature. You can modify the output to report the pairs of features with no changes made to them.
Algorithm
For each sequence: identify the features that match the criteria for Feature A identify the features that match the criteria for Feature B compare all pairs of features if they satisfy the requirements output them to the report file
Usage
Here is a sample session with twofeatWithout the -twoout option the output report contains just one feature for every pair of features found.
% twofeat tembl:hsfau Finds neighbouring pairs of features in sequences Type of first feature [*]: polyA_signal Type of second feature [*]: polyA_site The minimum distance between the features [0]: 10 The maximum distance between the features [0]: 50 Output report [hsfau.twofeat]: |
Go to the input files for this example
Go to the output files for this example
Example 2
The -twoout option makes the output report give the pairs of features found. The ouput report format type has been changed to display the full original pairs of faetures in GFF format.
% twofeat -twoout -rformat gff tembl:hsfau Finds neighbouring pairs of features in sequences Type of first feature [*]: polyA_signal Type of second feature [*]: polyA_site The minimum distance between the features [0]: 10 The maximum distance between the features [0]: 50 Output report [hsfau.twofeat]: |
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers:
[-sequence] seqall Sequence database USA
-atype string By default every feature in the feature
table is allowed. You can set this to be any
feature type you wish to allow.
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 allow more than one type,
separate their names with the character '|',
eg:
*UTR | intron
-btype string By default every feature in the feature
table is allowed. You can set this to be any
feature type you wish to allow.
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 allow more than one type,
separate their names with the character '|',
eg:
*UTR | intron
-minrange integer If this is greater or equal to 'maxrange',
then no min or max range is specified
-maxrange integer If this is less than or equal to 'minrange',
then no min or max range is specified
[-outfile] report Output report file name
Additional (Optional) qualifiers (* if not always prompted):
-asource string By default any feature source in the feature
table is allowed. You can set this to match
any feature source you wish to allow.
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 allow more than one source,
separate their names with the character '|',
eg:
gene* | embl
-asense menu By default any feature sense is allowed. You
can set this to match the required sense.
-aminscore float If this is greater than or equal to the
maximum score, then any score is allowed.
-amaxscore float If this is less than or equal to the maximum
score, then any score is permitted.
-atag 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 allowed. You can set this to match
any feature tag you wish to allow.
The tag may be wildcarded by using '*'.
If you wish to allow more than one tag,
separate their names with the character '|',
eg:
gene | label
-avalue 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 allowed. You can set this
to match any feature tag value you wish to
allow.
The tag value may be wildcarded by using
'*'.
If you wish to allow more than one tag
value, separate their names with the
character '|', eg:
pax* | 10
-bsource string By default any feature source in the feature
table is allowed. You can set this to match
any feature source you wish to allow.
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 allow more than one source,
separate their names with the character '|',
eg:
gene* | embl
-bsense menu By default any feature sense is allowed. You
can set this to match the required sense.
-bminscore float If this is greater than or equal to the
maximum score, then any score is allowed.
-bmaxscore float If this is less than or equal to the maximum
score, then any score is permitted.
-btag 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 allowed. You can set this to match
any feature tag you wish to allow.
The tag may be wildcarded by using '*'.
If you wish to allow more than one tag,
separate their names with the character '|',
eg:
gene | label
-bvalue 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 allowed. You can set this
to match any feature tag value you wish to
allow.
The tag value may be wildcarded by using
'*'.
If you wish to allow more than one tag
value, separate their names with the
character '|', eg:
pax* | 10
-overlap menu This allows you to specify the allowed
overlaps of the features A and B.
You can allow any or no overlaps, specify
that they must or must not overlap, that one
must or must not be wholly enclosed within
another feature.
-rangetype menu This allows you to specify the positions
from which the allowed minimum or maximum
distance between the features is measured
-sense menu This allows you to specify the required
sense that the two features must be on. This
is ignored (always 'Any') when looking at
protein sequence features.
-order menu This allows you to specify the required
order of the two features. The order is
measured from the start positions of the
features. This criterion is always applied
despite the specified overlap type required.
-twoout toggle If you set this to be true, then the two
features themselves will be written out. If
it is left as false, then a single feature
will be written out covering the two
features you found.
* -typeout string If you have specified that the pairs of
features that are found should be reported
as one feature in the ouput, then you can
specify the 'type' name of the new feature
here. By default every feature in the
feature table is allowed. 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. If you
specify an invalid feature type name, then
the default name 'misc_feature' is used.
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-outfile" associated qualifiers
-rformat2 string Report format
-rname2 string Base file name
-rextension2 string File name extension
-rdirectory2 string Output directory
-raccshow2 boolean Show accession number in the report
-rdesshow2 boolean Show description in the report
-rscoreshow2 boolean Show the score in the report
-rusashow2 boolean Show the full USA in the report
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report deaths
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required | ||||||||||||
| -atype | By default every feature in the feature table is allowed. You can set this to be any feature type you wish to allow. 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 allow more than one type, separate their names with the character '|', eg: *UTR | intron | Any string is accepted | * | ||||||||||||
| -btype | By default every feature in the feature table is allowed. You can set this to be any feature type you wish to allow. 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 allow more than one type, separate their names with the character '|', eg: *UTR | intron | Any string is accepted | * | ||||||||||||
| -minrange | If this is greater or equal to 'maxrange', then no min or max range is specified | Any integer value | 0 | ||||||||||||
| -maxrange | If this is less than or equal to 'minrange', then no min or max range is specified | Any integer value | 0 | ||||||||||||
| [-outfile] (Parameter 2) |
Output report file name | Report output file | |||||||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||||||
| -asource | By default any feature source in the feature table is allowed. You can set this to match any feature source you wish to allow. 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 allow more than one source, separate their names with the character '|', eg: gene* | embl | Any string is accepted | * | ||||||||||||
| -asense | By default any feature sense is allowed. You can set this to match the required sense. |
|
0 | ||||||||||||
| -aminscore | If this is greater than or equal to the maximum score, then any score is allowed. | Any numeric value | 0.0 | ||||||||||||
| -amaxscore | If this is less than or equal to the maximum score, then any score is permitted. | Any numeric value | 0.0 | ||||||||||||
| -atag | 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 allowed. You can set this to match any feature tag you wish to allow. The tag may be wildcarded by using '*'. If you wish to allow more than one tag, separate their names with the character '|', eg: gene | label | Any string is accepted | * | ||||||||||||
| -avalue | 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 allowed. You can set this to match any feature tag value you wish to allow. The tag value may be wildcarded by using '*'. If you wish to allow more than one tag value, separate their names with the character '|', eg: pax* | 10 | Any string is accepted | * | ||||||||||||
| -bsource | By default any feature source in the feature table is allowed. You can set this to match any feature source you wish to allow. 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 allow more than one source, separate their names with the character '|', eg: gene* | embl | Any string is accepted | * | ||||||||||||
| -bsense | By default any feature sense is allowed. You can set this to match the required sense. |
|
0 | ||||||||||||
| -bminscore | If this is greater than or equal to the maximum score, then any score is allowed. | Any numeric value | 0.0 | ||||||||||||
| -bmaxscore | If this is less than or equal to the maximum score, then any score is permitted. | Any numeric value | 0.0 | ||||||||||||
| -btag | 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 allowed. You can set this to match any feature tag you wish to allow. The tag may be wildcarded by using '*'. If you wish to allow more than one tag, separate their names with the character '|', eg: gene | label | Any string is accepted | * | ||||||||||||
| -bvalue | 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 allowed. You can set this to match any feature tag value you wish to allow. The tag value may be wildcarded by using '*'. If you wish to allow more than one tag value, separate their names with the character '|', eg: pax* | 10 | Any string is accepted | * | ||||||||||||
| -overlap | This allows you to specify the allowed overlaps of the features A and B. You can allow any or no overlaps, specify that they must or must not overlap, that one must or must not be wholly enclosed within another feature. |
|
A | ||||||||||||
| -rangetype | This allows you to specify the positions from which the allowed minimum or maximum distance between the features is measured |
|
N | ||||||||||||
| -sense | This allows you to specify the required sense that the two features must be on. This is ignored (always 'Any') when looking at protein sequence features. |
|
A | ||||||||||||
| -order | This allows you to specify the required order of the two features. The order is measured from the start positions of the features. This criterion is always applied despite the specified overlap type required. |
|
A | ||||||||||||
| -twoout | If you set this to be true, then the two features themselves will be written out. If it is left as false, then a single feature will be written out covering the two features you found. | Toggle value Yes/No | No | ||||||||||||
| -typeout | If you have specified that the pairs of features that are found should be reported as one feature in the ouput, then you can specify the 'type' name of the new feature here. By default every feature in the feature table is allowed. 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. If you specify an invalid feature type name, then the default name 'misc_feature' is used. | Any string is accepted | misc_feature | ||||||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||||||
| (none) | |||||||||||||||
Input file format
twofeat reads any normal sequence USAs.Input files for usage example
'tembl:hsfau' is a sequence entry in the example nucleic acid database 'tembl'
Database entry: tembl:hsfau
ID HSFAU standard; RNA; HUM; 518 BP.
XX
AC X65923;
XX
SV X65923.1
XX
DT 13-MAY-1992 (Rel. 31, Created)
DT 23-SEP-1993 (Rel. 37, Last updated, Version 10)
XX
DE H.sapiens fau mRNA
XX
KW fau gene.
XX
OS Homo sapiens (human)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN [1]
RP 1-518
RA Michiels L.M.R.;
RT ;
RL Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
RL L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN [2]
RP 1-518
RX MEDLINE; 93368957.
RA Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT " fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT an antisense sequences in the Finkel-Biskis-Reilly murine sarcoma virus";
RL Oncogene 8:2537-2546(1993).
XX
DR SWISS-PROT; P35544; UBIM_HUMAN.
DR SWISS-PROT; Q05472; RS30_HUMAN.
XX
FH Key Location/Qualifiers
FH
FT source 1..518
FT /chromosome="11q"
FT /db_xref="taxon:9606"
FT /organism="Homo sapiens"
FT /tissue_type="placenta"
FT /clone_lib="cDNA"
FT /clone="pUIA 631"
FT /map="13"
FT misc_feature 57..278
FT /note="ubiquitin like part"
FT CDS 57..458
FT /db_xref="SWISS-PROT:P35544"
FT /db_xref="SWISS-PROT:Q05472"
FT /gene="fau"
FT /protein_id="CAA46716.1"
FT /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT misc_feature 98..102
FT /note="nucleolar localization signal"
FT misc_feature 279..458
FT /note="S30 part"
FT polyA_signal 484..489
FT polyA_site 509
XX
SQ Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc 60
agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg 120
cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc 180
tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc 240
tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc 300
gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga 360
agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca 420
cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc 480
tctaataaaa aagccactta gttcagtcaa aaaaaaaa 518
//
|
Output file format
The output is a standard EMBOSS report file.
The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq
See: http://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats.
twofeat outputs a report format file. The default format is table
Output files for usage example
File: hsfau.twofeat
########################################
# Program: twofeat
# Rundate: Fri Jul 15 2005 12:00:00
# Report_format: table
# Report_file: hsfau.twofeat
########################################
#=======================================
#
# Sequence: HSFAU from: 1 to: 518
# HitCount: 1
#=======================================
Start End Score starta enda startb endb
484 509 0.000 484 489 509 509
#---------------------------------------
#---------------------------------------
|
Output files for usage example 2
File: hsfau.twofeat
##gff-version 2.0 ##date 2005-07-15 ##Type DNA HSFAU HSFAU EMBL polyA_signal 484 489 0.000 + . Sequence "HSFAU.6" HSFAU EMBL polyA_site 509 509 0.000 + . Sequence "HSFAU.7" ; FeatFlags "0x40" |
Data files
None.Notes
It can't find features that are not in the input sequences. It has no way of checking whether the input features are correct or not. Remember this when you are searching public databases.References
None.Warnings
None.Diagnostic Error Messages
None.Exit status
It always exits with status 0.Known bugs
There is a slight memory leak that must be fixed at some time. This does no affect the results.See also
| Program name | Description |
|---|---|
| coderet | Extract CDS, mRNA and translations from feature tables |
| extractfeat | Extract features from a sequence |
| maskfeat | Mask off features of a sequence |
| showfeat | Show features of a sequence |
Author(s)
Gary Williams (gwilliam © rfcgr.mrc.ac.uk)MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK