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EMBOSS: complex |
% complex -omnia Input sequence: embl:* Output sequence [hscad5.fasta]: Window length [100]: Step size [5]: Minimum word length [4]: Maximum word length [6]: Output file [hscad5.complex]: do embComWriteFile HSCAD5 3170 HSD 781 HSEGL1 3919 HSFAU 518 HSFOS 6210 HSEF2 3075 HSHT 1658 CEZK637 40699 PDRHOD 1675 ECLAC 7477 ECLACA 1832 ECLACI 1113 ECLACY 1500 ECLACZ 3078 PAAMIB 1212 PAAMIE 1065 PAAMIR 2167 PAAMIS 1130 MMAM 366 RNOPS 1493 RNU68037 1218 HHTETRA 1272 100 5 0 4 6
Mandatory qualifiers (* if not always prompted): [-sequence] seqall Sequence database USA * -outseq seqoutall Output sequence(s) USA -lwin integer Window length -step integer the displacement of the window over the sequence -jmin integer Minimum word length -jmax integer Maximum word length -outfile outfile Output file name * -ujtable outfile UjTable temporary file name Optional qualifiers: (none) Advanced qualifiers: -omnia bool calculate over a set of sequences -sim integer calculate the linguistic complexity by comparison with a number of simulations having a uniform distribution of bases -freq bool execute the simulation of a sequence based on the base frequency of the original sequence -print bool generate a file named UjTable containing the values of Uj for each word j in the real sequence(s) and in any simulated sequences |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
-outseq | Output sequence(s) USA | Writeable sequence(s) | <sequence>.format |
-lwin | Window length | Any integer value | 100 |
-step | the displacement of the window over the sequence | Any integer value | 5 |
-jmin | Minimum word length | Integer from 2 to 20 | 4 |
-jmax | Maximum word length | Integer from 2 to 50 | 6 |
-outfile | Output file name | Output file | <sequence>.complex |
-ujtable | UjTable temporary file name | Output file | complex.ujtable |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-omnia | calculate over a set of sequences | Yes/No | No |
-sim | calculate the linguistic complexity by comparison with a number of simulations having a uniform distribution of bases | Any integer value | 0 |
-freq | execute the simulation of a sequence based on the base frequency of the original sequence | Yes/No | No |
generate a file named UjTable containing the values of Uj for each word j in the real sequence(s) and in any simulated sequences | Yes/No | No |
Sequence TEMBL:HHTETRA contains repeats and is included in the test database for repeat analysis.
Length of window : 100 jmin : 4 jmax : 6 step : 5 Execution without simulation ---------------------------------------------------------------------------- | | | | | | number of | name of | length of | value of | | sequence | sequence | sequence | complexity | | | | | | ---------------------------------------------------------------------------- 1 HSCAD5 3170 0.6921 2 HSD 781 0.6991 3 HSEGL1 3919 0.6618 4 HSFAU 518 0.6739 5 HSFOS 6210 0.6681 6 HSEF2 3075 0.6925 7 HSHT 1658 0.7314 8 CEZK637 40699 0.6307 9 PDRHOD 1675 0.6201 10 ECLAC 7477 0.7137 11 ECLACA 1832 0.6916 12 ECLACI 1113 0.7480 13 ECLACY 1500 0.6801 14 ECLACZ 3078 0.7278 15 PAAMIB 1212 0.6596 16 PAAMIE 1065 0.6418 17 PAAMIR 2167 0.6562 18 PAAMIS 1130 0.6989 19 MMAM 366 0.7163 20 RNOPS 1493 0.6571 21 RNU68037 1218 0.6381 22 HHTETRA 1272 0.3114
Program name | Description |
---|---|
banana | Bending and curvature plot in B-DNA |
btwisted | Calculates the twisting in a B-DNA sequence |
dan | Calculates DNA RNA/DNA melting temperature |