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fuzznuc |
Function
Nucleic acid pattern searchDescription
fuzznuc uses PROSITE style patterns to search nucleotide sequences.Patterns are specifications of a (typically short) length of sequence to be found. They can specify a search for an exact sequence or they can allow various ambiguities, matches to variable lengths of sequence and repeated subsections of the sequence.
fuzznuc intelligently selects the optimum searching algorithm to use, depending on the complexity of the search pattern specified.
Usage
Here is a sample session with fuzznuc
% fuzznuc Nucleic acid pattern search Input sequence(s): tembl:hhtetra Search pattern: AAGCTT Number of mismatches [0]: Output report [hhtetra.fuzznuc]: |
Go to the input files for this example
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers:
[-sequence] seqall Sequence database USA
-pattern string The standard IUPAC one-letter codes for the
nucleotides are used.
The symbol `n' is used for a position where
any nucleotide is accepted.
Ambiguities are indicated by listing the
acceptable nucleotides for a given position,
between square parentheses `[ ]'. For
example: [ACG] stands for A or C or G.
Ambiguities are also indicated by listing
between a pair of curly brackets `{ }' the
nucleotides that are not accepted at a given
position. For example: {AG} stands for any
nucleotides except A and G.
Each element in a pattern is separated from
its neighbor by a `-'. (Optional in
fuzznuc).
Repetition of an element of the pattern can
be indicated by following that element with
a numerical value or a numerical range
between parenthesis. Examples: N(3)
corresponds to N-N-N, N(2,4) corresponds to
N-N or N-N-N or N-N-N-N.
When a pattern is restricted to either the
5' or 3' end of a sequence, that pattern
either starts with a `<' symbol or
respectively ends with a `>' symbol.
A period ends the pattern. (Optional in
fuzznuc).
For example, [CG](5)TG{A}N(1,5)C
-mismatch integer Number of mismatches
[-outfile] report Output report file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-complement boolean Search complementary strand
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
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
| -pattern | The standard IUPAC one-letter codes for the nucleotides are used. The symbol `n' is used for a position where any nucleotide is accepted. Ambiguities are indicated by listing the acceptable nucleotides for a given position, between square parentheses `[ ]'. For example: [ACG] stands for A or C or G. Ambiguities are also indicated by listing between a pair of curly brackets `{ }' the nucleotides that are not accepted at a given position. For example: {AG} stands for any nucleotides except A and G. Each element in a pattern is separated from its neighbor by a `-'. (Optional in fuzznuc). Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis. Examples: N(3) corresponds to N-N-N, N(2,4) corresponds to N-N or N-N-N or N-N-N-N. When a pattern is restricted to either the 5' or 3' end of a sequence, that pattern either starts with a `<' symbol or respectively ends with a `>' symbol. A period ends the pattern. (Optional in fuzznuc). For example, [CG](5)TG{A}N(1,5)C | Any string is accepted | An empty string is accepted |
| -mismatch | Number of mismatches | Integer 0 or more | 0 |
| [-outfile] (Parameter 2) |
Output report file name | Report output file | |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -complement | Search complementary strand | Boolean value Yes/No | No |
Input file format
fuzznuc reads in normal nucleic acid sequence USAs.Input files for usage example
'tembl:hhtetra' is a sequence entry in the example nucleic acid database 'tembl'
Database entry: tembl:hhtetra
ID HHTETRA standard; DNA; VRL; 1272 BP.
XX
AC L46634; L46689;
XX
SV L46634.1
XX
DT 06-NOV-1995 (Rel. 45, Created)
DT 04-MAR-2000 (Rel. 63, Last updated, Version 3)
XX
DE Human herpesvirus 7 (clone ED132'1.2) telomeric repeat region.
XX
KW telomeric repeat.
XX
OS Human herpesvirus 7
OC Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Betaherpesvirinae.
XX
RN [1]
RP 1-1272
RX MEDLINE; 96079055.
RA Secchiero P., Nicholas J., Deng H., Xiaopeng T., van Loon N., Ruvolo V.R.,
RA Berneman Z.N., Reitz M.S. Jr., Dewhurst S.;
RT "Identification of human telomeric repeat motifs at the genome termini of
RT human herpesvirus 7: structural analysis and heterogeneity";
RL J. Virol. 69(12):8041-8045(1995).
XX
FH Key Location/Qualifiers
FH
FT source 1..1272
FT /db_xref="taxon:10372"
FT /organism="Human herpesvirus 7"
FT /strain="JI"
FT /clone="ED132'1.2"
FT repeat_region 207..928
FT /note="long and complex repeat region composed of various
FT direct repeats, including TAACCC (TRS), degenerate copies
FT of TRS motifs and a 14-bp repeat, TAGGGCTGCGGCCC"
FT misc_signal 938..998
FT /note="pac2 motif"
FT misc_feature 1009
FT /note="right genome terminus (...ACA)"
XX
SQ Sequence 1272 BP; 346 A; 455 C; 222 G; 249 T; 0 other;
aagcttaaac tgaggtcaca cacgacttta attacggcaa cgcaacagct gtaagctgca 60
ggaaagatac gatcgtaagc aaatgtagtc ctacaatcaa gcgaggttgt agacgttacc 120
tacaatgaac tacacctcta agcataacct gtcgggcaca gtgagacacg cagccgtaaa 180
ttcaaaactc aacccaaacc gaagtctaag tctcacccta atcgtaacag taaccctaca 240
actctaatcc tagtccgtaa ccgtaacccc aatcctagcc cttagcccta accctagccc 300
taaccctagc tctaacctta gctctaactc tgaccctagg cctaacccta agcctaaccc 360
taaccgtagc tctaagttta accctaaccc taaccctaac catgaccctg accctaaccc 420
tagggctgcg gccctaaccc tagccctaac cctaacccta atcctaatcc tagccctaac 480
cctagggctg cggccctaac cctagcccta accctaaccc taaccctagg gctgcggccc 540
taaccctaac cctagggctg cggcccgaac cctaacccta accctaaccc taaccctagg 600
gctgcggccc taaccctaac cctagggctg cggccctaac cctaacccta gggctgcggc 660
ccgaacccta accctaaccc taaccctagg gctgcggccc taaccctaac cctagggctg 720
cggccctaac cctaacccta actctagggc tgcggcccta accctaaccc taaccctaac 780
cctagggctg cggcccgaac cctagcccta accctaaccc tgaccctgac cctaacccta 840
accctaaccc taaccctaac cctaacccta accctaaccc taaccctaac cctaacccta 900
accctaaccc taaccctaac cctaaccccg cccccactgg cagccaatgt cttgtaatgc 960
cttcaaggca ctttttctgc gagccgcgcg cagcactcag tgaaaaacaa gtttgtgcac 1020
gagaaagacg ctgccaaacc gcagctgcag catgaaggct gagtgcacaa ttttggcttt 1080
agtcccataa aggcgcggct tcccgtagag tagaaaaccg cagcgcggcg cacagagcga 1140
aggcagcggc tttcagactg tttgccaagc gcagtctgca tcttaccaat gatgatcgca 1200
agcaagaaaa atgttctttc ttagcatatg cgtggttaat cctgttgtgg tcatcactaa 1260
gttttcaagc tt 1272
//
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Pattern specification
Patterns for fuzznuc are based on the format of pattern used in the PROSITE database, with the difference that the terminating dot '.' and the hyphens, '-', between the characters are optional.The PROSITE pattern definition from the PROSITE documentation (amended to refer to nucleic acid sequences, not proteins) follows.
- The standard IUPAC one-letter codes for the nucleotides are used.
- The symbol `n' is used for a position where any nucleotide is accepted.
- Ambiguities are indicated by listing the acceptable nucleotides for a given position, between square parentheses `[ ]'. For example: [ACG] stands for A or C or G.
- Ambiguities are also indicated by listing between a pair of curly brackets `{ }' the nucleotides that are not accepted at a given position. For example: {AG} stands for any nucleotides except A and G.
- Each element in a pattern is separated from its neighbor by a `-'. (Optional in fuzznuc).
- Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis. Examples: N(3) corresponds to N-N-N, N(2,4) corresponds to N-N or N-N-N or N-N-N-N.
- When a pattern is restricted to either the 5' or 3' end of a sequence, that pattern either starts with a `<' symbol or respectively ends with a `>' symbol.
- A period ends the pattern. (Optional in fuzznuc).
- All other characters, including spaces are not allowed.
For example, in the EMBL entry ECLAC you can look for the pattern:
[CG](5)TG{A}N(1,5)C
This searches for "C or G" 5 times, followed by T and G, then anything except A, then any base (1 to 5 times) before a C.
You can use ambiguity codes for nucleic acid searches but not within [] or {} as they expand to bracketed counterparts. For example, "s" is expanded to "[GC]" therefore [S] would be expanded to [[GC]] which is illegal.
Note the use of X is reserved for proteins. You must use N for nucleic acids to refer to any base.
The search is case-independent, so 'AAA' matches 'aaa'.
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.
By default fuzznuc writes a 'seqtable' report file.
Output files for usage example
File: hhtetra.fuzznuc
########################################
# Program: fuzznuc
# Rundate: Fri Jul 15 2005 12:00:00
# Report_format: seqtable
# Report_file: hhtetra.fuzznuc
########################################
#=======================================
#
# Sequence: HHTETRA from: 1 to: 1272
# HitCount: 2
#
# Pattern: AAGCTT
# Mismatch: 0
# Complement: No
#
#=======================================
Start End Mismatch Sequence
1 6 . aagctt
1267 1272 . aagctt
#---------------------------------------
#---------------------------------------
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Data files
None.Notes
None.References
None.Warnings
None.Diagnostic Error Messages
None.Exit status
It always exits with a status of 0.Known bugs
None.See also
| Program name | Description |
|---|---|
| dreg | Regular expression search of a nucleotide sequence |
| fuzztran | Protein pattern search after translation |
| marscan | Finds MAR/SAR sites in nucleic sequences |
Other EMBOSS programs allow you to search for regular expression patterns but may be less easy for the user who has never used regular expressions before:
- dreg - Regular expression search of a nucleotide sequence
- preg - Regular expression search of a protein sequence
Author(s)
Alan Bleasby (ajb © ebi.ac.uk)European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
History
Written (2000) - Alan Bleasby'-usa' added (13 March 2001) - Gary Williams