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EMBOSS: newcpgreport |
See the FTP site: ftp://ftp.ebi.ac.uk/pub/databases/cpgisle/ for the finished database.
% newcpgreport Input sequence: embl:rnu68037 Window size [100]: Shift increment [1]: Minimum Length [200]: Minimum observed/expected [0.6]: Minimum percentage [50.]: Output file [rnu68037.newcpgreport]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA -window integer Window size -shift integer Shift increment -minlen integer Minimum Length -minoe float Minimum observed/expected -minpc float Minimum percentage [-outfile] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: -[no]obsexp bool Show observed/expected threshold line -[no]cg bool Show CpG rich regions -[no]pc bool Show percentage line |
| Mandatory qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
| -window | Window size | Integer 1 or more | 100 |
| -shift | Shift increment | Integer 1 or more | 1 |
| -minlen | Minimum Length | Integer 1 or more | 200 |
| -minoe | Minimum observed/expected | Number from 0.000 to 10.000 | 0.6 |
| -minpc | Minimum percentage | Number from 0.000 to 100.000 | 50. |
| [-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.newcpgreport |
| Optional qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced qualifiers | Allowed values | Default | |
| -[no]obsexp | Show observed/expected threshold line | Yes/No | Yes |
| -[no]cg | Show CpG rich regions | Yes/No | Yes |
| -[no]pc | Show percentage line | Yes/No | Yes |
ID RNU68037 1118 BP. XX DE CpG Island report. XX CC Obs/Exp ratio > 0.60. CC % C + % G > 50.00. CC Length > 200. XX FH Key Location/Qualifiers FT CpG island 157..389 FT /size=232 FT /Sum C+G=152 FT /Percent CG=65.24 FT /ObsExp=0.73 FT CpG island 654..963 FT /size=309 FT /Sum C+G=206 FT /Percent CG=66.45 FT /ObsExp=0.96 FT numislands 2 //
| 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 |
| newcpgseek | Reports CpG rich regions |
| 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 |