|   | wordcount | 
| % wordcount tembl:u68037 -wordsize=3 Counts words of a specified size in a DNA sequence Output file [u68037.wordcount]: | 
Go to the input files for this example
Go to the output files for this example
| 
   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
   -wordsize           integer    [4] Word size (Integer 2 or more)
  [-outfile]           outfile    [*.wordcount] Output file name
   Additional (Optional) qualifiers:
   -mincount           integer    [1] Minimum word count to report (Integer 1
                                  or more)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:
   "-sequence" 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
   "-outfile" associated qualifiers
   -odirectory2        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 | |
|---|---|---|---|
| [-sequence] (Parameter 1) | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | 
| -wordsize | Word size | Integer 2 or more | 4 | 
| [-outfile] (Parameter 2) | Output file name | Output file | <*>.wordcount | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| -mincount | Minimum word count to report | Integer 1 or more | 1 | 
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
| 
ID   U68037; SV 1; linear; mRNA; STD; ROD; 1218 BP.
XX
AC   U68037;
XX
DT   23-SEP-1996 (Rel. 49, Created)
DT   04-MAR-2000 (Rel. 63, Last updated, Version 2)
XX
DE   Rattus norvegicus EP1 prostanoid receptor mRNA, complete cds.
XX
KW   .
XX
OS   Rattus norvegicus (Norway rat)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea;
OC   Muridae; Murinae; Rattus.
XX
RN   [1]
RP   1-1218
RA   Abramovitz M., Boie Y.;
RT   "Cloning of the rat EP1 prostanoid receptor";
RL   Unpublished.
XX
RN   [2]
RP   1-1218
RA   Abramovitz M., Boie Y.;
RT   ;
RL   Submitted (26-AUG-1996) to the EMBL/GenBank/DDBJ databases.
RL   Biochemistry & Molecular Biology, Merck Frosst Center for Therapeutic
RL   Research, P. O. Box 1005, Pointe Claire - Dorval, Quebec H9R 4P8, Canada
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1218
FT                   /organism="Rattus norvegicus"
FT                   /strain="Sprague-Dawley"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:10116"
FT   CDS             1..1218
FT                   /codon_start=1
FT                   /product="EP1 prostanoid receptor"
FT                   /note="family 1 G-protein coupled receptor"
FT                   /db_xref="GOA:P70597"
FT                   /db_xref="InterPro:IPR000276"
FT                   /db_xref="InterPro:IPR000708"
FT                   /db_xref="InterPro:IPR001244"
FT                   /db_xref="InterPro:IPR008365"
FT                   /db_xref="UniProtKB/Swiss-Prot:P70597"
FT                   /protein_id="AAB07735.1"
FT                   /translation="MSPYGLNLSLVDEATTCVTPRVPNTSVVLPTGGNGTSPALPIFSM
FT                   TLGAVSNVLALALLAQVAGRLRRRRSTATFLLFVASLLAIDLAGHVIPGALVLRLYTAG
FT                   RAPAGGACHFLGGCMVFFGLCPLLLGCGMAVERCVGVTQPLIHAARVSVARARLALALL
FT                   AAMALAVALLPLVHVGHYELQYPGTWCFISLGPPGGWRQALLAGLFAGLGLAALLAALV
FT                   CNTLSGLALLRARWRRRRSRRFRENAGPDDRRRWGSRGLRLASASSASSITSTTAALRS
FT                   SRGGGSARRVHAHDVEMVGQLVGIMVVSCICWSPLLVLVVLAIGGWNSNSLQRPLFLAV
FT                   RLASWNQILDPWVYILLRQAMLRQLLRLLPLRVSAKGGPTELSLTKSAWEASSLRSSRH
FT                   SGFSHL"
XX
SQ   Sequence 1218 BP; 162 A; 397 C; 387 G; 272 T; 0 other;
     atgagcccct acgggcttaa cctgagccta gtggatgagg caacaacgtg tgtaacaccc        60
     agggtcccca atacatctgt ggtgctgcca acaggcggta acggcacatc accagcgctg       120
     cctatcttct ccatgacgct gggtgctgtg tccaacgtgc tggcgctggc gctgctggcc       180
     caggttgcag gcagactgcg gcgccgccgc tcgactgcca ccttcctgtt gttcgtcgcc       240
     agcctgcttg ccatcgacct agcaggccat gtgatcccgg gcgccttggt gcttcgcctg       300
     tatactgcag gacgtgcgcc cgctggcggg gcctgtcatt tcctgggcgg ctgtatggtc       360
     ttctttggcc tgtgcccact tttgcttggc tgtggcatgg ccgtggagcg ctgcgtgggt       420
     gtcacgcagc cgctgatcca cgcggcgcgc gtgtccgtag cccgcgcacg cctggcacta       480
     gccctgctgg ccgccatggc tttggcagtg gcgctgctgc cactagtgca cgtgggtcac       540
     tacgagctac agtaccctgg cacttggtgt ttcattagcc ttgggcctcc tggaggttgg       600
     cgccaggcgt tgcttgcggg cctcttcgcc ggccttggcc tggctgcgct ccttgccgca       660
     ctagtgtgta atacgctcag cggcctggcg ctccttcgtg cccgctggag gcggcgtcgc       720
     tctcgacgtt tccgagagaa cgcaggtccc gatgatcgcc ggcgctgggg gtcccgtgga       780
     ctccgcttgg cctccgcctc gtctgcgtca tccatcactt caaccacagc tgccctccgc       840
     agctctcggg gaggcggctc cgcgcgcagg gttcacgcac acgacgtgga aatggtgggc       900
     cagctcgtgg gcatcatggt ggtgtcgtgc atctgctgga gccccctgct ggtattggtg       960
     gtgttggcca tcgggggctg gaactctaac tccctgcagc ggccgctctt tctggctgta      1020
     cgcctcgcgt cgtggaacca gatcctggac ccatgggtgt acatcctgct gcgccaggct      1080
     atgctgcgcc aacttcttcg cctcctaccc ctgagggtta gtgccaaggg tggtccaacg      1140
     gagctgagcc taaccaagag tgcctgggag gccagttcac tgcgtagctc ccggcacagt      1200
     ggcttcagcc acttgtga                                                    1218
//
 | 
| ctg 54 gcc 53 tgg 53 ggc 51 gct 47 cgc 47 gtg 40 tgc 39 cct 38 gcg 36 cca 29 ggg 26 tcc 25 ctt 25 cag 25 ccc 24 ggt 24 ctc 23 tgt 23 ccg 22 gca 22 cgt 22 cac 22 agc 21 ttg 19 acg 19 cgg 19 tcg 18 ttc 17 cat 17 agg 17 gag 16 act 16 gtc 16 aac 15 tct 14 atc 14 gga 14 tca 13 cta 13 atg 12 acc 11 gta 11 gtt 11 aca 10 tga 10 caa 10 tac 10 gac 9 tag 9 agt 9 ttt 8 cga 7 gat 6 taa 6 aga 5 tat 5 gaa 4 aat 3 tta 3 ata 3 att 3 aag 2 aaa 1 | 
The file simply consists of two columns, separated by spaces or TAB characters.
The first column consists of all the possible words of size wordsize. The second column consists of the count of those words in the input sequence.
| Program name | Description | 
|---|---|
| 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 | 
| compseq | Count composition of dimer/trimer/etc words in a sequence | 
| dan | Calculates DNA RNA/DNA melting temperature | 
| freak | Residue/base frequency table or plot | 
| isochore | Plots isochores in large DNA sequences | 
| sirna | Finds siRNA duplexes in mRNA |