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fuzztran
Function
Protein pattern search after translation
Description
fuzztran uses PROSITE style protein patterns to search nucleic acid
sequences translated in the specified frame(s).
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.
fuzztran intelligently selects the optimum searching algorithm to use,
depending on the complexity of the search pattern specified.
Usage
Here is a sample session with fuzztran
% fuzztran -opt
Protein pattern search after translation
Input nucleotide sequence(s): tembl:Z46957
Search pattern: RA
Translation frames
1 : 1
2 : 2
3 : 3
F : Forward three frames
-1 : -1
-2 : -2
-3 : -3
R : Reverse three frames
6 : All six frames
Frame(s) to translate [1]: f
Genetic codes
0 : Standard
1 : Standard (with alternative initiation codons)
2 : Vertebrate Mitochondrial
3 : Yeast Mitochondrial
4 : Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiropl
asma
5 : Invertebrate Mitochondrial
6 : Ciliate Macronuclear and Dasycladacean
9 : Echinoderm Mitochondrial
10 : Euplotid Nuclear
11 : Bacterial
12 : Alternative Yeast Nuclear
13 : Ascidian Mitochondrial
14 : Flatworm Mitochondrial
15 : Blepharisma Macronuclear
16 : Chlorophycean Mitochondrial
21 : Trematode Mitochondrial
22 : Scenedesmus obliquus
23 : Thraustochytrium Mitochondrial
Code to use [0]:
Output report [z46957.fuzztran]:
Go to the input files for this example
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers:
[-sequence] seqall Nucleotide sequence(s) filename and optional
format, or reference (input USA)
-pattern pattern The standard IUPAC one-letter codes for the
amino acids are used.
The symbol 'x' is used for a position where
any amino acid is accepted.
Ambiguities are indicated by listing the
acceptable amino acids for a given position,
between square parentheses '[ ]'. For
example: [ALT] stands for Ala or Leu or Thr.
Ambiguities are also indicated by listing
between a pair of curly brackets '{ }' the
amino acids that are not accepted at a gven
position. For example: {AM} stands for any
amino acid except Ala and Met.
Each element in a pattern is separated from
its neighbor by a '-'. (Optional in
fuzztran)
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: x(3)
corresponds to x-x-x, x(2,4) corresponds to
x-x or x-x-x or x-x-x-x.
When a pattern is restricted to either the
N- or C-terminal of a sequence, that pattern
either starts with a '<' symbol or
respectively ends with a '>' symbol.
A period ends the pattern. (Optional in
fuzztran).
For example, [DE](2)HS{P}X(2)PX(2,4)C
[-outfile] report [*.fuzztran] Output report file name
Additional (Optional) qualifiers:
-frame menu [1] Frame(s) to translate (Values: 1 (1); 2
(2); 3 (3); F (Forward three frames); -1
(-1); -2 (-2); -3 (-3); R (Reverse three
frames); 6 (All six frames))
-table menu [0] Code to use (Values: 0 (Standard); 1
(Standard (with alternative initiation
codons)); 2 (Vertebrate Mitochondrial); 3
(Yeast Mitochondrial); 4 (Mold, Protozoan,
Coelenterate Mitochondrial and
Mycoplasma/Spiroplasma); 5 (Invertebrate
Mitochondrial); 6 (Ciliate Macronuclear and
Dasycladacean); 9 (Echinoderm
Mitochondrial); 10 (Euplotid Nuclear); 11
(Bacterial); 12 (Alternative Yeast Nuclear);
13 (Ascidian Mitochondrial); 14 (Flatworm
Mitochondrial); 15 (Blepharisma
Macronuclear); 16 (Chlorophycean
Mitochondrial); 21 (Trematode
Mitochondrial); 22 (Scenedesmus obliquus);
23 (Thraustochytrium Mitochondrial))
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
"-pattern" associated qualifiers
-pformat string File format
-pmismatch integer Pattern mismatch
-pname string Pattern base 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
-rmaxall2 integer Maximum total hits to report
-rmaxseq2 integer Maximum hits to report for one sequence
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 dying program messages
Input file format
fuzztran reads in normal nucleic acid sequence USAs.
Input files for usage example
'tembl:Z46957' is a sequence entry in the example nucleic acid
database 'tembl'
Database entry: tembl:Z46957
ID Z46957; SV 1; linear; mRNA; STD; ROD; 1493 BP.
XX
AC Z46957;
XX
DT 20-DEC-1994 (Rel. 42, Created)
DT 18-APR-2005 (Rel. 83, Last updated, Version 9)
XX
DE R.norvegicus mRNA for rhodopsin.
XX
KW rhodopsin.
XX
OS Rattus norvegicus (Norway rat)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea;
OC Muridae; Murinae; Rattus.
XX
RN [1]
RP 1-1493
RX DOI; 10.1074/jbc.271.20.11710.
RX PUBMED; 8662634.
RA Huber A., Sander P.H., Paulsen R.;
RT "Phosphorylation of the InaD gene product, a photoreceptor membrane protei
n
RT required for recovery of visual excitation";
RL J. Biol. Chem. 271(20):11710-11717(1996).
XX
RN [2]
RP 1-1493
RA Huber A.;
RT ;
RL Submitted (20-DEC-1994) to the EMBL/GenBank/DDBJ databases.
RL Huber A., Universitaet Karlsruhe, Zoologie I, Kornblumenstr. 13, 76128
RL Karlsruhe, Germany
XX
DR EMBL-ALIGN; ALIGN_000323.
XX
FH Key Location/Qualifiers
FH
FT source 1..1493
FT /organism="Rattus norvegicus"
FT /strain="Sprague-Dawley"
FT /mol_type="mRNA"
FT /dev_stage="adult"
FT /clone_lib="rat retinal library"
FT /clone="pRO4"
FT /cell_type="rod"
FT /tissue_type="retina"
FT /db_xref="taxon:10116"
FT 5'UTR 1..83
FT CDS 84..1130
FT /product="rhodopsin"
FT /function="phototransduction"
FT /db_xref="GOA:P51489"
FT /db_xref="UniProtKB/Swiss-Prot:P51489"
FT /citation=[1]
FT /protein_id="CAA87081.1"
FT /translation="MNGTEGPNFYVPFSNITGVVRSPFEQPQYYLAEPWQFSMLAAYM
F
FT LLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYF
V
FT FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWV
M
FT ALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFF
C
FT YGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQG
S
FT NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTTLCCGKNPLGDDEASATASK
T
FT ETSQVAPA"
FT 3'UTR 1128..1493
XX
SQ Sequence 1493 BP; 309 A; 475 C; 365 G; 344 T; 0 other;
ggagccgtag gtagctgagc tcgccaggca gccttggtct ctgtctacga acagcccgtg 6
0
gggcagcctc aagggccgca gccatgaacg gcacagaggg ccccaatttt tatgtgccct 12
0
tctccaacat cacgggcgtg gtgcgcagcc cctttgagca gccgcagtac tacctggcgg 18
0
agccatggca gttctccatg ctggcagcct acatgttcct gctcatcgtg ctgggcttcc 24
0
ccatcaactt cctcacgctc tacgtcaccg tacagcacaa gaagctgcgc acaccactca 30
0
actacatcct gctcaacttg gctgtggctg acctcttcat ggtcttcgga ggattcacca 36
0
ccaccctcta cacctcactg catggctact ttgtctttgg gcccacaggc tgcaaccttg 42
0
agggcttctt tgccaccctt ggaggtgaaa tcggcctgtg gtccctggta gtcctggcca 48
0
ttgagcgcta cgtggtggtc tgcaagccca tgagcaactt ccgctttggg gagaatcatg 54
0
ccattatggg tgtggccttc acctgggtca tggcgttggc ctgtgctgct cccccactgg 60
0
ttggctggtc caggtacatc cccgagggca tgcagtgttc atgtgggatt gactactata 66
0
cactcaagcc tgaggtcaac aatgagtcct tcgtcatcta catgttcgtg gtccacttca 72
0
ccatccccat gatcgtcatc ttcttctgct acgggcagct ggtcttcacc gtcaaggagg 78
0
ccgccgccca gcaacaggag tcggctacca ctcagaaggc agagaaggaa gtcacgcgca 84
0
tggtcatcat catggtcatc ttcttcctga tctgctggct tccctatgcc agtgtggcca 90
0
tgtacatctt tacccaccag ggctccaact tcggccccat cttcatgacc cttcccgctt 96
0
tctttgctaa gaccgcctcc atctacaacc caatcatcta catcatgatg aacaagcagt 102
0
tccggaactg catgctcacc acgctctgct gcggcaagaa tccactggga gatgatgagg 108
0
cctctgccac tgcctccaag acggagacca gccaggtggc tccagcctaa gcctggccag 114
0
agactgtggc tgactgtagg agtctcctgt ccccactcac cccagccaca gcccccacca 120
0
ggagcagcac ccgttggaat gaggtcatgc aggctccctc agtgttcttt tctttgtttt 126
0
taatgaattc atgaaagcaa aatgaggctc cccactcaac agggacagcc tgacaaagga 132
0
catccatcca ccaagacccc cagcctggag tccccaattc ccgggggcca gcgggatctg 138
0
tacccctccc ctcagcttgt gtctcaggaa catgacaagt gtcccggctt acggctaagt 144
0
gtctaggaca gaatggaaca catagtagct gattaataaa tgctacctgg atg 149
3
//
Pattern specification
Patterns for fuzztran 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 follows.
* The standard IUPAC one-letter codes for the amino acids are used.
* The symbol `x' is used for a position where any amino acid is
accepted.
* Ambiguities are indicated by listing the acceptable amino acids
for a given position, between square parentheses `[ ]'. For
example: [ALT] stands for Ala or Leu or Thr.
* Ambiguities are also indicated by listing between a pair of curly
brackets `{ }' the amino acids that are not accepted at a given
position. For example: {AM} stands for any amino acid except Ala
and Met.
* Each element in a pattern is separated from its neighbor by a `-'.
(Optional in fuzztran).
* 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: x(3) corresponds to x-x-x, x(2,4)
corresponds to x-x or x-x-x or x-x-x-x.
* When a pattern is restricted to either the N- or C-terminal of a
sequence, that pattern either starts with a `<' symbol or
respectively ends with a `>' symbol.
* A period ends the pattern. (Optional in fuzztran).
* All other characters, including spaces are not allowed.
For example, you can look for the pattern:
[DE](2)HS{P}X(2)PX(2,4)C
This means: Two Asps or Glus in any order followed by His, Ser, any
residue other then Pro, then two of any residue followed by Pro
followed by two to four of any residue followed by Cys.
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 fuzztran writes a 'table' report file.
Output files for usage example
File: z46957.fuzztran
########################################
# Program: fuzztran
# Rundate: Sun 15 Jul 2007 12:00:00
# Commandline: fuzztran
# -options
# -sequence tembl:Z46957
# -pattern RA
# -frame f
# Report_format: table
# Report_file: z46957.fuzztran
########################################
#=======================================
#
# Sequence: Z46957 from: 1 to: 1493
# HitCount: 9
#
# Pattern_name Mismatch Pattern
# pattern1 0 RA
# TransTable: 0
# Frames: F
#
#=======================================
Start End Score Pattern_name Mismatch Frame PStart PEnd Translation
97 102 2 pattern1 . 1 33 34 RA
133 138 2 pattern1 . 1 45 46 RA
421 426 2 pattern1 . 1 141 142 RA
625 630 2 pattern1 . 1 209 210 RA
835 840 2 pattern1 . 1 279 280 RA
919 924 2 pattern1 . 1 307 308 RA
227 232 2 pattern1 . 2 76 77 RA
752 757 2 pattern1 . 2 251 252 RA
72 77 2 pattern1 . 3 24 25 RA
#---------------------------------------
#---------------------------------------
#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 9
#---------------------------------------
The columns of data are as follows:
1. Start - the start position of the pattern in the nucleic acids
sequence.
2. End - the end position of the pattern in the nucleic acids
sequence.
3. Score - the score of the match.
4. Mismatch - the number of mismatches .
5. Frame - the translation frame that the pattern match occurs in.
6. PStart - the start position of the match in the resulting protein
sequence.
7. PEnd - the end position of the match in the resulting protein
sequence.
8. Translation - the protein sequence that is matched.
Data files
EMBOSS data files are distributed with the application and stored in
the standard EMBOSS data directory, which is defined by the EMBOSS
environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called ".embossdata".
Files for all EMBOSS runs can be put in the user's home directory, or
again in a subdirectory called ".embossdata".
The directories are searched in the following order:
* . (your current directory)
* .embossdata (under your current directory)
* ~/ (your home directory)
* ~/.embossdata
The Genetic Code data files are based on the NCBI genetic code tables.
Their names and descriptions are:
EGC.0
Standard (Differs from GC.1 in that it only has initiation site
'AUG')
EGC.1
Standard
EGC.2
Vertebrate Mitochodrial
EGC.3
Yeast Mitochondrial
EGC.4
Mold, Protozoan, Coelenterate Mitochondrial and
Mycoplasma/Spiroplasma
EGC.5
Invertebrate Mitochondrial
EGC.6
Ciliate Macronuclear and Dasycladacean
EGC.9
Echinoderm Mitochondrial
EGC.10
Euplotid Nuclear
EGC.11
Bacterial
EGC.12
Alternative Yeast Nuclear
EGC.13
Ascidian Mitochondrial
EGC.14
Flatworm Mitochondrial
EGC.15
Blepharisma Macronuclear
EGC.16
Chlorophycean Mitochondrial
EGC.21
Trematode Mitochondrial
EGC.22
Scenedesmus obliquus
EGC.23
Thraustochytrium Mitochondrial
The format of these files is very simple.
It consists of several lines of optional comments, each starting with
a '#' character.
These are followed the line: 'Genetic Code [n]', where 'n' is the
number of the genetic code file.
This is followed by the description of the code and then by four lines
giving the IUPAC one-letter code of the translated amino acid, the
start codons (indicdated by an 'M') and the three bases of the codon,
lined up one on top of the other.
For example:
------------------------------------------------------------------------------
# Genetic Code Table
#
# Obtained from: http://www.ncbi.nlm.nih.gov/collab/FT/genetic_codes.html
# and: http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c
#
# Differs from Genetic Code [1] only in that the initiation sites have been
# changed to only 'AUG'
Genetic Code [0]
Standard
AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
------------------------------------------------------------------------------
Notes
None.
References
None.
Warnings
When translating using non-standard genetic code table, always check
the table carefully for deviations from your particular organism's
code.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None.
See also
Program name Description
antigenic Finds antigenic sites in proteins
digest Protein proteolytic enzyme or reagent cleavage digest
dreg Regular expression search of a nucleotide sequence
epestfind Finds PEST motifs as potential proteolytic cleavage sites
fuzznuc Nucleic acid pattern search
fuzzpro Protein pattern search
helixturnhelix Report nucleic acid binding motifs
marscan Finds MAR/SAR sites in nucleic sequences
oddcomp Find protein sequence regions with a biased composition
patmatdb Search a protein sequence with a motif
patmatmotifs Search a PROSITE motif database with a protein sequence
pepcoil Predicts coiled coil regions
preg Regular expression search of a protein sequence
pscan Scans proteins using PRINTS
sigcleave Reports protein signal cleavage sites
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
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
|
