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wordcount |
Displays all the words of the specified length with the number of times it occurs.
% wordcount tembl:rnu68037 -wordsize=3 Counts words of a specified size in a DNA sequence Output file [rnu68037.wordcount]: |
Go to the input files for this example
Go to the output files for this example
Mandatory qualifiers: [-sequence] sequence Sequence USA -wordsize integer Word size -outfile outfile Output file name Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence USA | Readable sequence | Required |
-wordsize | Word size | Integer 2 or more | 4 |
-outfile | Output file name | Output file | <sequence>.wordcount |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
ID RNU68037 standard; RNA; ROD; 1218 BP. XX AC U68037; XX SV U68037.1 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; Rodentia; Sciurognathi; 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 XX RN [1] RP 1-1218 RA Abramovitz M., Boie Y.; RT "Cloning of the rat EP1 prostanoid receptor"; RL Unpublished.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 DR SWISS-PROT; P70597; PE21_RAT. XX FH Key Location/Qualifiers FH FT source 1..1218 FT /db_xref="taxon:10116" FT /organism="Rattus norvegicus" FT /strain="Sprague-Dawley" FT CDS 1..1218 FT /codon_start=1 FT /db_xref="SWISS-PROT:P70597" FT /note="family 1 G-protein coupled receptor" FT /product="EP1 prostanoid receptor" 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 tgg 53 gcc 53 ggc 51 cgc 47 gct 47 gtg 40 tgc 39 cct 38 gcg 36 cca 29 ggg 26 cag 25 ctt 25 tcc 25 ggt 24 ccc 24 ctc 23 tgt 23 gca 22 cgt 22 ccg 22 cac 22 agc 21 acg 19 ttg 19 cgg 19 tcg 18 ttc 17 cat 17 agg 17 act 16 gtc 16 gag 16 aac 15 gga 14 atc 14 tct 14 tca 13 cta 13 atg 12 gtt 11 acc 11 gta 11 aca 10 tac 10 tga 10 caa 10 gac 9 agt 9 tag 9 ttt 8 cga 7 gat 6 taa 6 tat 5 aga 5 gaa 4 aat 3 ata 3 tta 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 | Counts the 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 |