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complex |
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% complex -omnia Find the linguistic complexity in nucleotide sequences Input nucleotide sequence(s): tembl:x* Window length [100]: Step size [5]: Minimum word length [4]: Maximum word length [6]: Program complex output file [x59796.complex]: output sequence(s) [x59796.fasta]: |
Go to the input files for this example
Go to the output files for this example
Find the linguistic complexity in nucleotide sequences
Version: EMBOSS:6.3.1
Standard (Mandatory) qualifiers (* if not always prompted):
[-sequence] seqall Nucleotide sequence(s) filename and optional
format, or reference (input USA)
-lwin integer [100] Window length (Integer 1 or more)
-step integer [5] Displacement of the window over the
sequence (Integer 1 or more)
-jmin integer [4] Minimum word length (Integer from 2 to
20)
-jmax integer [6] Maximum word length (Integer from 2 to
50)
[-outfile] outfile [*.complex] Program complex output file
* -outseq seqoutall [
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
seqall | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| -lwin | integer | Window length | Integer 1 or more | 100 |
| -step | integer | Displacement of the window over the sequence | Integer 1 or more | 5 |
| -jmin | integer | Minimum word length | Integer from 2 to 20 | 4 |
| -jmax | integer | Maximum word length | Integer from 2 to 50 | 6 |
| [-outfile] (Parameter 2) |
outfile | Program complex output file | Output file | <*>.complex |
| -outseq | seqoutall | Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -omnia | toggle | Calculate over a set of sequences | Toggle value Yes/No | No |
| -sim | integer | Calculate the linguistic complexity by comparison with a number of simulations having a uniform distribution of bases | Any integer value | 0 |
| -freq | boolean | Execute the simulation of a sequence based on the base frequency of the original sequence | Boolean value Yes/No | No |
| boolean | Generate a file named UjTable containing the values of Uj for each word j in the real sequence(s) and in any simulated sequences | Boolean value Yes/No | No | |
| -ujtablefile | outfile | Program complex temporary output file | Output file | complex.ujtable |
| Associated qualifiers | ||||
| "-sequence" associated seqall qualifiers | ||||
| -sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 |
| -send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |
| -sid1 -sid_sequence |
string | Entryname | Any string | |
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |
| -fformat1 -fformat_sequence |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
| "-outfile" associated outfile qualifiers | ||||
| -odirectory2 -odirectory_outfile |
string | Output directory | Any string | |
| "-ujtablefile" associated outfile qualifiers | ||||
| -odirectory | string | Output directory | Any string | |
| "-outseq" associated seqoutall qualifiers | ||||
| -osformat | string | Output seq format | Any string | |
| -osextension | string | File name extension | Any string | |
| -osname | string | Base file name | Any string | |
| -osdirectory | string | Output directory | Any string | |
| -osdbname | string | Database name to add | Any string | |
| -ossingle | boolean | Separate file for each entry | Boolean value Yes/No | N |
| -oufo | string | UFO features | Any string | |
| -offormat | string | Features format | Any string | |
| -ofname | string | Features file name | Any string | |
| -ofdirectory | string | Output directory | Any string | |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
| -version | boolean | Report version number and exit | Boolean value Yes/No | N |
|
|
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 X59796 3170 0.6921
2 X65923 518 0.6739
3 X65921 2016 0.7105
4 X51466 3075 0.6925
5 X07523 1658 0.7314
6 X03487 512 0.5609
7 X03488 1132 0.7217
8 X07797 1675 0.6201
9 X51872 1832 0.6916
10 X77160 1212 0.6596
11 X13776 2167 0.6562
12 X77161 1130 0.6989
|
>X59796 X59796.1 H.sapiens mRNA for cadherin-5 ctccactcacgctcagccctggacggacaggcagtccaacggaacagaaacatccctcag cccacaggcacgatctgttcctcctgggaagatgcagaggctcatgatgctcctcgccac atcgggcgcctgcctgggcctgctggcagtggcagcagtggcagcagcaggtgctaaccc tgcccaacgggacacccacagcctgctgcccacccaccggcgccaaaagagagattggat ttggaaccagatgcacattgatgaagagaaaaacacctcacttccccatcatgtaggcaa gatcaagtcaagcgtgagtcgcaagaatgccaagtacctgctcaaaggagaatatgtggg caaggtcttccgggtcgatgcagagacaggagacgtgttcgccattgagaggctggaccg ggagaatatctcagagtaccacctcactgctgtcattgtggacaaggacactggcgaaaa cctggagactccttccagcttcaccatcaaagttcatgacgtgaacgacaactggcctgt gttcacgcatcggttgttcaatgcgtccgtgcctgagtcgtcggctgtggggacctcagt catctctgtgacagcagtggatgcagacgaccccactgtgggagaccacgcctctgtcat gtaccaaatcctgaaggggaaagagtattttgccatcgataattctggacgtattatcac aataacgaaaagcttggaccgagagaagcaggccaggtatgagatcgtggtggaagcgcg agatgcccagggcctccggggggactcgggcacggccaccgtgctggtcactctgcaaga catcaatgacaacttccccttcttcacccagaccaagtacacatttgtcgtgcctgaaga 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ggccggagcgctgaccctgctattcgcttttacctatctgtgggtggccgccaaccagtt cctcgag >X77161 X77161.1 Pseudomonas aeruginosa (PAC1) amiS gene. gagccgtccgcctgagcgatccgggccgaccagaacaataacaagaggggtatcgtcatc atgctgggactggttctgctgtacgttggcgcggtgctgtttctcaatgccgtctggttg ctgggcaagatcagcggtcgggaggtggcggtgatcaacttcctggtcggcgtgctgagc gcctgcgtcgcgttctacctgatcttttccgcagcagccgggcagggctcgctgaaggcc ggagcgctgaccctgctattcgcttttacctatctgtgggtggccgccaaccagttcctc gaggtggacggcaagggcctcggctggttctgcctgttcgtcagcctcaccgcctgcacc gtggcgatcgagtcgttcgccggcgccagtggtccgttcggcctgtggaacgcggtcaac tggacagtctgggcgttgctctggttctgtttcttcctgctgctggggctgtcccgcggc atccagaagccggtggcctacctgaccctggccagcgccatattcaccgcctggttgccc ggcctgctgctgctcggacaggtgctcaaggcatagcaggaagtcggaaagggatgacgg cttgccgccatcccgtcccttccgaacgcctagccgagcggccagttgatcaccacgacg gcgtcgttgtagtcgttgtcggtgccgtcttcagagccgaccagggcgaagttcagctcg ttggtcaggattacctgtgccgagaccagatccgaggggcggccgttgacgctgacctgg acctgtaccttgccactgctgccggagttgagcacctgggtgccgatgacggcgttattg gtgctttgcccgctgaaggtcgcggccgtgctcgttgttgaccagcacgttcaccgtctg ggttccggacgagttggcgaaggcggtgacgccggaacctggttgttggcgggaagggtg aacactccttgtggttgccatggtggtatctccactgaatacctggccccttccttttca ggcagccgtctggcgcgcggtatggcgtgtcgggagaaatccgcagtccttggcggcagg cgatgcgcaggcaggaaggacgcatcgttcagccaatctacgccgtcgac |
| Program name | Description |
|---|---|
| banana | Plot bending and curvature data for B-DNA |
| btwisted | Calculate the twisting in a B-DNA sequence |
| chaos | Draw a chaos game representation plot for a nucleotide sequence |
| compseq | Calculate the composition of unique words in sequences |
| dan | Calculates nucleic acid melting temperature |
| density | Draw a nucleic acid density plot |
| freak | Generate residue/base frequency table or plot |
| isochore | Plots isochores in DNA sequences |
| sirna | Finds siRNA duplexes in mRNA |
| wordcount | Count and extract unique words in molecular sequence(s) |