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EMBOSS: wordcount |
Displays all the words of the specified length with the number of times it occurs.
% wordcount embl:rnu68037 -wordsize=3 Counts words of a specified size in a DNA sequence Output file [rnu68037.wordcount]:
Mandatory qualifiers: [-sequence] sequence Sequence USA -wordsize integer Word size -outfile outfile Output file name Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help bool 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) |
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 |