freak

 

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Function

Generate residue/base frequency table or plot

Description

freak reads one or more sequences and a set of bases or residues to search for. It then calculates the frequency of these bases/residues in a window as it moves along the sequence. The frequency is output to a data file or (optionally) plotted.

Algorithm

The frequency of bases/residues is calculated in a window that is moved along the sequence. The window size and stepping value (number of positions the window is moved along each time) may be specified.

Usage

Here is a sample session with freak


% freak tembl:x65923 
Generate residue/base frequency table or plot
Residue letters [gc]: 
Output file [x65923.freak]: 

Go to the input files for this example
Go to the output files for this example

Command line arguments

Generate residue/base frequency table or plot
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-seqall]            seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
   -letters            string     [gc] Residue letters (Any string)
*  -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tek, tekt, none, data, xterm, png, gif, pdf,
                                  svg)
*  -outfile            outfile    [*.freak] Output file name

   Additional (Optional) qualifiers:
   -step               integer    [1] Stepping value (Any integer value)
   -window             integer    [30] Averaging window (Any integer value)

   Advanced (Unprompted) qualifiers:
   -plot               toggle     [N] Produce graphic

   Associated qualifiers:

   "-seqall" 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
   -scircular1         boolean    Sequence is circular
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-graph" associated qualifiers
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         string     Output directory

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-seqall]
(Parameter 1)
seqall Sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) Required
-letters string Residue letters Any string gc
-graph xygraph Graph type EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg EMBOSS_GRAPHICS value, or x11
-outfile outfile Output file name Output file <*>.freak
Additional (Optional) qualifiers
-step integer Stepping value Any integer value 1
-window integer Averaging window Any integer value 30
Advanced (Unprompted) qualifiers
-plot toggle Produce graphic Toggle value Yes/No No
Associated qualifiers
"-seqall" associated seqall qualifiers
-sbegin1
-sbegin_seqall
integer Start of each sequence to be used Any integer value 0
-send1
-send_seqall
integer End of each sequence to be used Any integer value 0
-sreverse1
-sreverse_seqall
boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_seqall
boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_seqall
boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_seqall
boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_seqall
boolean Make lower case Boolean value Yes/No N
-supper1
-supper_seqall
boolean Make upper case Boolean value Yes/No N
-scircular1
-scircular_seqall
boolean Sequence is circular Boolean value Yes/No N
-sformat1
-sformat_seqall
string Input sequence format Any string  
-iquery1
-iquery_seqall
string Input query fields or ID list Any string  
-ioffset1
-ioffset_seqall
integer Input start position offset Any integer value 0
-sdbname1
-sdbname_seqall
string Database name Any string  
-sid1
-sid_seqall
string Entryname Any string  
-ufo1
-ufo_seqall
string UFO features Any string  
-fformat1
-fformat_seqall
string Features format Any string  
-fopenfile1
-fopenfile_seqall
string Features file name Any string  
"-graph" associated xygraph qualifiers
-gprompt boolean Graph prompting Boolean value Yes/No N
-gdesc string Graph description Any string  
-gtitle string Graph title Any string  
-gsubtitle string Graph subtitle Any string  
-gxtitle string Graph x axis title Any string  
-gytitle string Graph y axis title Any string  
-goutfile string Output file for non interactive displays Any string  
-gdirectory string Output directory Any string  
"-outfile" associated outfile qualifiers
-odirectory string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

freak reads one or more nucleotide or protein sequences.

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

Input files for usage example

'tembl:x65923' is a sequence entry in the example nucleic acid database 'tembl'

Database entry: tembl:x65923

ID   X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC   X65923;
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   18-APR-2005 (Rel. 83, Last updated, Version 11)
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; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-518
RA   Michiels L.M.R.;
RT   ;
RL   Submitted (29-APR-1992) to the INSDC.
RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN   [2]
RP   1-518
RX   PUBMED; 8395683.
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 sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8(9):2537-2546(1993).
XX
DR   Ensembl-Gn; ENSG00000149806; Homo_sapiens.
DR   Ensembl-Tr; ENST00000279259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000434372; Homo_sapiens.
DR   Ensembl-Tr; ENST00000525297; Homo_sapiens.
DR   Ensembl-Tr; ENST00000526555; Homo_sapiens.
DR   Ensembl-Tr; ENST00000527548; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529639; Homo_sapiens.
DR   Ensembl-Tr; ENST00000531743; Homo_sapiens.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /organism="Homo sapiens"
FT                   /chromosome="11q"
FT                   /map="13"
FT                   /mol_type="mRNA"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /tissue_type="placenta"
FT                   /db_xref="taxon:9606"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /gene="fau"
FT                   /db_xref="GDB:135476"
FT                   /db_xref="GOA:P35544"
FT                   /db_xref="GOA:P62861"
FT                   /db_xref="H-InvDB:HIT000322806.14"
FT                   /db_xref="HGNC:3597"
FT                   /db_xref="InterPro:IPR000626"
FT                   /db_xref="InterPro:IPR006846"
FT                   /db_xref="InterPro:IPR019954"
FT                   /db_xref="InterPro:IPR019955"
FT                   /db_xref="InterPro:IPR019956"
FT                   /db_xref="PDB:2L7R"
FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
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

If -plot is specified, graphics output is produced.

The output is to the specified graphics device.

The results can be output in one of several formats by using the command-line qualifier -graph xxx, where 'xxx' is replaced by the name of the required device. Support depends on the availability of third-party software packages.

The device names that output to a file are: ps (postscript), cps (colourps), png, gif, pdf, svg, hpgl, hp7470, hp7580, das, data.

The other available device names are: meta, x11 (xwindows), tek (tek4107t), tekt (tektronix), xterm, text.

Output can be turned off by specifying none (null).

See: http://emboss.sf.net/docs/themes/GraphicsDevices.html for further information on supported devices.

Output files for usage example

File: x65923.freak

FREAK of X65923 from 1 to 518 Window 30 Step 1

1          0.500000
2          0.533333
3          0.566667
4          0.533333
5          0.533333
6          0.566667
7          0.566667
8          0.566667
9          0.600000
10         0.633333
11         0.633333
12         0.666667
13         0.666667
14         0.666667
15         0.666667
16         0.633333
17         0.666667
18         0.633333
19         0.633333
20         0.633333
21         0.666667
22         0.666667
23         0.700000
24         0.733333
25         0.700000
26         0.666667
27         0.633333
28         0.600000
29         0.566667
30         0.600000
31         0.633333
32         0.600000
33         0.600000
34         0.633333
35         0.600000
36         0.600000
37         0.566667
38         0.566667
39         0.533333
40         0.533333
41         0.500000
42         0.500000
43         0.500000
44         0.500000
45         0.533333
46         0.566667
47         0.566667
48         0.600000


  [Part of this file has been deleted for brevity]

439        0.433333
440        0.400000
441        0.366667
442        0.333333
443        0.333333
444        0.300000
445        0.333333
446        0.366667
447        0.400000
448        0.366667
449        0.333333
450        0.300000
451        0.333333
452        0.333333
453        0.333333
454        0.333333
455        0.300000
456        0.300000
457        0.300000
458        0.300000
459        0.300000
460        0.266667
461        0.266667
462        0.233333
463        0.233333
464        0.266667
465        0.300000
466        0.333333
467        0.300000
468        0.333333
469        0.333333
470        0.333333
471        0.333333
472        0.366667
473        0.333333
474        0.333333
475        0.333333
476        0.300000
477        0.300000
478        0.300000
479        0.333333
480        0.333333
481        0.300000
482        0.300000
483        0.266667
484        0.266667
485        0.266667
486        0.266667
487        0.266667
488        0.266667
489        0.266667

The output consists of a title line and then two columns containing the position of the start of the window and then the frequency in that window of the bases or residues being searched for.

Data files

None.

Notes

The default set of bases is cg which will calculate the frequency of G + C bases within the default moving window of 30 bases.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description
backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq Back-translate a protein sequence to a nucleotide sequence
banana Plot bending and curvature data for B-DNA
btwisted Calculate the twisting in a B-DNA sequence
chaos Draw a chaos game representation plot for a nucleotide sequence
compseq Calculate the composition of unique words in sequences
dan Calculate nucleic acid melting temperature
density Draw a nucleic acid density plot
emowse Search protein sequences by digest fragment molecular weight
isochore Plot isochores in DNA sequences
mwcontam Find weights common to multiple molecular weights files
mwfilter Filter noisy data from molecular weights file
oddcomp Identify proteins with specified sequence word composition
pepdigest Report on protein proteolytic enzyme or reagent cleavage sites
pepinfo Plot amino acid properties of a protein sequence in parallel
pepstats Calculate statistics of protein properties
wordcount Count and extract unique words in molecular sequence(s)

Author(s)

Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Written (Aug 2000) Alan Bleasby

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None