freak Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. 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:6.4.0.0 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 -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 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 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 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 sequence 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="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="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 Calculates nucleic acid melting temperature density Draw a nucleic acid density plot emowse Search protein sequences by digest fragment molecular weight isochore Plots 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 Reports on protein proteolytic enzyme or reagent cleavage sites pepinfo Plot amino acid properties of a protein sequence in parallel pepstats Calculates 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 (c) 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