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EMBOSS: newcpgseek |
% newcpgseek Input sequence: embl:rnu68037 CpG score [17]: Output file [rnu68037.newcpgseek]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA -score integer CpG score [-outfile] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: (none) |
| Mandatory qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
| -score | CpG score | Integer from 1 to 200 | 17 |
| [-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.newcpgseek |
| Optional qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced qualifiers | Allowed values | Default | |
| (none) | |||
NEWCPGSEEK of RNU68037 from 1 to 1218 with score > 17 Begin End Score CpG %CG CG/GC * 96 1032 630 87 66.1 0.65 1072 1100 26 3 62.1 0.00 1183 1193 26 2 72.7 2.00 -------------------------------------------
| Program name | Description |
|---|---|
| chaos | Create a chaos game representation plot for a sequence |
| chips | Codon usage statistics |
| codcmp | Codon usage table comparison |
| compseq | Counts the composition of dimer/trimer/etc words in a sequence |
| cpgplot | Plot CpG rich areas |
| cpgreport | Reports all CpG rich regions |
| cusp | Create a codon usage table |
| diffseq | Find differences (SNPs) between nearly identical sequences |
| dotmatcher | Displays a thresholded dotplot of two sequences |
| dotpath | Displays a non-overlapping wordmatch dotplot of two sequences |
| dottup | Displays a wordmatch dotplot of two sequences |
| einverted | Finds DNA inverted repeats |
| equicktandem | Finds tandem repeats |
| etandem | Looks for tandem repeats in a nucleotide sequence |
| freak | Residue/base frequency table or plot |
| geecee | Calculates the fractional GC content of nucleic acid sequences |
| isochore | Plots isochores in large DNA sequences |
| newcpgreport | Report CpG rich areas |
| palindrome | Looks for inverted repeats in a nucleotide sequence |
| polydot | Displays all-against-all dotplots of a set of sequences |
| redata | Search REBASE for enzyme name, references, suppliers etc |
| restrict | Finds restriction enzyme cleavage sites |
| showseq | Display a sequence with features, translation etc |
| silent | Silent mutation RE scan |
| tfscan | Scans DNA sequences for transcription factors |
| wobble | Wobble base plot |
| wordcount | Counts words of a specified size in a DNA sequence |