|   | freak | 
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.
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.
| % 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
| 
   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 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. 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
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-seqall] (Parameter 1) | Sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | 
| -letters | Residue letters | Any string is accepted | gc | 
| -graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11 | 
| -outfile | Output file name | Output file | <*>.freak | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| -step | Stepping value | Any integer value | 1 | 
| -window | Averaging window | Any integer value | 30 | 
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -plot | Produce graphic | Toggle value Yes/No | No | 
| 
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="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
//
 | 
| 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.
The default set of bases is cg which will calculate the frequency of G + C bases within the default moving window of 30 bases.
| 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 | 
| charge | Draw a protein charge plot | 
| checktrans | Reports STOP codons and ORF statistics of a protein | 
| compseq | Calculate the composition of unique words in sequences | 
| dan | Calculates nucleic acid melting temperature | 
| density | Draw a nucleic acid density plot | 
| emowse | Search protein sequences by digest fragment molecular weight | 
| iep | Calculate the isoelectric point of proteins | 
| isochore | Plots isochores in DNA sequences | 
| mwcontam | Find weights common to multiple molecular weights files | 
| mwfilter | Filter noisy data from molecular weights file | 
| octanol | Draw a White-Wimley protein hydropathy plot | 
| pepinfo | Plot amino acid properties of a protein sequence in parallel | 
| pepstats | Calculates statistics of protein properties | 
| pepwindow | Draw a Kyte-Doolittle hydropathy plot for a protein sequence | 
| pepwindowall | Draw Kyte-Doolittle hydropathy plot for a protein alignment | 
| sirna | Finds siRNA duplexes in mRNA | 
| wordcount | Count and extract unique words in DNA sequence(s) |