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freak
Function
Residue/base frequency table or plot
Description
freak takes one or more sequences as input 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.
The default set of bases is 'cg' which will calculate the frequency of
'G' + 'C' bases within the default moving window of 30 bases.
Usage
Here is a sample session with freak
% freak tembl:x65923
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
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 is
accepted)
* -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tekt, tek, none, data, xterm, png, gif)
* -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
-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
"-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 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
freak reads normal sequence USAs.
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 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 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 sequences in the Finkel-Biskis-Reilly murine sarcoma virus";
RL Oncogene 8(9):2537-2546(1993).
XX
DR H-InvDB; HIT000322806.
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="HGNC:3597"
FT /db_xref="UniProtKB/Swiss-Prot:P35544"
FT /db_xref="UniProtKB/Swiss-Prot:P62861"
FT /protein_id="CAA46716.1"
FT /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLA
G
FT APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKT
G
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 6
0
agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg 12
0
cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc 18
0
tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc 24
0
tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc 30
0
gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga 36
0
agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca 42
0
cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc 48
0
tctaataaaa aagccactta gttcagtcaa aaaaaaaa 51
8
//
Output file format
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 ouput 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
None.
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 codons
backtranseq Back translate a protein sequence
banana Bending and curvature plot in B-DNA
btwisted Calculates the twisting in a B-DNA sequence
chaos Create a chaos game representation plot for a sequence
charge Protein charge plot
checktrans Reports STOP codons and ORF statistics of a protein
compseq Count composition of dimer/trimer/etc words in a sequence
dan Calculates DNA RNA/DNA melting temperature
emowse Protein identification by mass spectrometry
iep Calculates the isoelectric point of a protein
isochore Plots isochores in large DNA sequences
mwcontam Shows molwts that match across a set of files
mwfilter Filter noisy molwts from mass spec output
octanol Displays protein hydropathy
pepinfo Plots simple amino acid properties in parallel
pepstats Protein statistics
pepwindow Displays protein hydropathy
pepwindowall Displays protein hydropathy of a set of sequences
sirna Finds siRNA duplexes in mRNA
wordcount Counts words of a specified size in a DNA sequence
Author(s)
Alan Bleasby (ajb ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
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
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