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